Plot summary of Xenoblade Chronicles 2

This page describes a plot summary of Xenoblade Chronicles 2. It is not a full description nor a complete novelization, but simply an overview of major events.

Chapter 1: Encounters
A small Titan rests upon the Cloud Sea, as his only inhabitant, a young salvager, fishes up an old crate from the depths. The two of them, Rex and "Gramps", banter over Rex's salvaging trade as Rex provides exposition. In the middle of the Cloud Sea of Alrest sits the World Tree. According to legend, people once lived with the Architect atop the tree, in a place called Elysium. But everyone was cast out, and are now forced to live on the Titans scattered across the clouds. And now, the Titans are slowly dying off. Rex is worried that eventually there'll be nowhere left for anyone to live.

Gramps takes Rex to the Argentum Trade Guild to sell his recent haul. He gets a paltry sale, but as usual sends a portion back home to Corinne in Fonsett Village. He then gets an unexpected summons from Chairman, who has an extremely lucrative job offer for him. Rex accepts immediately because he's a bit of a naïve dunce. Bana brings in the rest of the team to meet him, most of which are Drivers and s, which impresses Rex. Jin seems to be the leader, who tells Rex the job is to salvage something that's a long way down, and they need someone from Leftheria to do it (which Rex is). Malos questions whether Rex is a good pick because he's a child, so he attacks, and when Rex holds his own he relents. Nia (a Gormotti) seems to have the lowest rank, and gets snippy enough with Rex that her Blade Dromarch steps in. Malos also has a Blade, Sever, but he simply watches.

After Rex spends his advance payment to prepare for the job, and gets Gramps upset for running off on a job he knows nothing about, he boards the C.S.E.V. Maelstrom and they set out. While on watch, Rex spots a black ship possibly following them, but then gets into a conversation with Nia, explaining how he hopes to one day use his salvaging skills to find a way up onto the World Tree so people wouldn't have to fight for dwindling land and resources. Nia thinks this is a bit silly, but identifies with him having no parents, and decides he's alright. A storm brews as the ship reaches the salvage point, and Rex joins the crew in raising a huge Ancient Ship from the depths. Jin orders Rex to join the Driver team in searching the ship. They fight through a bunch of monsters and eventually reach the bottom deck. Jin orders Rex to open doors with "Addam's crest" on them, since he is supposedly one of the few who can. As a result, Rex gets ahead of the others and is the first to see a red sword in a pedestal, with what looks like a sleeping red-haired young lady trapped in the wall behind it. Jin and Malos recognize "the Aegis", while Nia does not. Rex is compelled to touch the green crystal in the sword, but the moment he does, Jin teleports behind him and fatally stabs him. Malos is disappointed but doesn't care, while Nia is greatly upset.

Rex finds himself is a grassy plain. He finds the lady there, who calls herself Pyra and says that he was killed, and is now in a memory of Elysium. But if he promises to take her to the real Elysium, she can revive him, which will make him her Driver. Rex agrees, and he reappears in the ship, with a new copy of the sword. Malos is carrying Pyra's body out of the ship when she awakens and causes chaos, and Rex arrives to help fight him. Malos is angered that Rex has become the Driver of the Aegis, but mostly blames himself for not noticing Rex's eyes, and reveals he's known Pyra for about five hundred years. In the battle, Nia and Dromarch switch sides to help Rex, as the following black ship arrives and opens fire. Gramps then also arrives, who Jin recognizes by his real name Azurda, and manages to rescue Rex, Pyra, Nia, and Dromarch as he gets shot. Jin decides this is fine for the moment, and to send Akhos after them.

Chapter 2: Aptitude
Bana hears from his spy that Rex got away with the Aegis. Worse, Malos failed to sink the Maelstrom and kill everyone, so he's out a huge chunk of insurance money. He predicts that they went to Gormott, so he calls his associate Consul Dughall to let him know.

Rex and Pyra wake up in the forest on an unknown Titan. They quickly find Gramps, who appears to die, but actually regenerates into a larval form that Rex carries in his helmet. They find Nia and Dromarch not long after and make camp. Gramps and Pyra speak with familiarity, about how Jin and Malos must be stopped, and whether Rex needs to be involved. The next morning, Nia says they're in Gormott and guides them to the capital Torigoth. When they arrive, Nia was angered by a poorly drawn wanted poster of her which she shredded, alongside wanted posters of Jin and Malos. They see a Driver recruitment event for the Mor Ardain military, with one native failing to awaken a Blade while another succeeds; it's explained that only some people are capable of turning Core Crystals into Blades and bonding with them. Rex is confused because that isn't how Pyra worked, which is apparently because "the Aegis" is some sort of special legendary Blade and so doesn't play by the normal rules.

As Nia is directing the group to an inn, Captain Padraig of the military finds them, which is trouble because Nia is part of the terrorist organization and Rex is an unregistered Driver. They resist arrest until Brighid, the strongest Blade in the empire, shows up. She buys the troops enough time to catch Nia and Dromarch in ether nets, and surrounds Rex and Pyra with a fire wall. She is then distracted when something from outside the fight explodes a water pipe and douses her, giving Rex and Pyra the chance to retaliate and escape. Brighid realizes that Pyra is the Aegis from being able to still use fire in the mess of all the water. While running from the troops, Rex and Pyra are approached by a Nopon, who hides them in his house so the troops lose them. Padraig reports what happened to Dughall, who is incensed that the dunderhead let Pyra get away, since his orders were to get the Blade with the green Core Crystal. He is then informed that Special Inquisitor Mòrag is on the way, which he is not pleased about.

The Nopon, Tora, says he's the one that caused the water pipe to burst (by accident). He was trying to save Rex because he wants to have a Driver friend. Rex wants to get after saving Nia right away, but he's convinced to eat first. Pyra makes food for them with her fire skills, but starts to get antsy when Tora asks about how she could still use fire with all the water previously, so Rex shuts him up. They change the subject to Nia, and ask around town for more information on what might have happened. They find that Nia is set to be executed soon, so they create a plan to sneak into Mòrag's Titan Battleship. Tora then reveals that since he cannot become a Driver properly, he's building an artificial Blade, and needs help (financially) to complete it. After some running around, he successfully completes Poppi, and the group begins their rescue attempt.

Infiltrating the Titan Battleship turns out to be fairly simple, and Poppi uses her Blade senses to find Dromarch. As Nia's Blade, he knows where she is, so they go get her with ease. Nia is busy recalling how Jin got her out of a similar predicament once when they reach her, and she is surprised and confused that this time it's Rex instead. They then move to escape the ship, but run into Dughall and his Blade Dolmes. Dughall tries to use Dolmes as a "meat"shield because of how Blades can regenerate with ease, but they still get the better of him. They are on the cusp of getting away when both Mòrag and Brighid block their way, revealing that the rumour of executing Nia was a bait to get them to show up. Mòrag says that she must take Pyra to ensure she can't go and sink three major Titans again like she did five hundred years ago. Rex doesn't buy it, and assumes she just wants Pyra as a weapon, so they fight. Mòrag is evidently the stronger side, but the party manage to bring down a water tower, which gives them an opening to escape again. She decides to let them go for the moment.

The group rests out in the wilderness. Nia tries to ditch them, but Rex talks about how he hopes to prove Elysium exists to try and stop the inevitable war for shrinking land, and needs people like her to help him. She is convinced to stay.

Chapter 3: Our Own War
The black ship that helped Malos and Jin, the, arrives at an unknown base. The aforementioned two exit it to see Akhos and his Blade Obrona. He says that two other accomplices, Mikhail and his "sister", are away at the moment. Obrona uses a long-range ether mapping ability to inform the group's plans; Jin will handle a shipment of Core Crystals heading to Indol, while the others will go for the group of Pyra, Dromarch, presumably Nia, and whoever else is with them.

Rex determines that since Gormott is currently the closest country to the World Tree, all they need is a ship to get there. Tora suggests "Unclepon" Umon, a shipbuilder (and old friend of his grampypon) that lives at Gormott's rear. They find him without trouble, and Tora manages to convince him to lend them a small Titan ship. They successfully reach the base of the World Tree, but find that the Cloud Sea seems to fall off a cliff surrounding it, forming a moat of emptiness. They are also attacked by a giant robotic snake that Pyra recognzies as Ophion, and she partly expects it to recognize her back. It stops attacking once Rex turns the boat around, but this leads them directly into the mouth of the Urayan Titan, and they get swallowed.

The group works to find a way out. Instead, they find, his Blade Roc, and two of his lackeys. Vandham recognizes Pyra as the Aegis, so he fights them, and defeats them due to Rex's inexperience with rationing a Blade's power. But this was only a test; he takes a shine to Rex and invites them to the nearby Garfont, a village of mercenaries and orphans. Vandham tries to impress upon Rex that being the Driver of the Aegis is no small thing, and that people less nice than he is will be after him. He then invites Rex on a job with him to check out something up near the Titan's blowhole, using Roc to clear out an ether miasma along the way, and teaching Rex how to improve his skill with the Anchor Shot. They find a dead Titan and are attacked by a large Arachno with a Blade of its own, and by killing it cause the Blade to vanish. Vandham explains that killing a Driver causes the Blade to revert to a dark Core Crystal, and will eventually glow again to be reborn with no memories of its past life. He then takes a fresh new crystal out of the dead Titan, saying that's where they come from. Pyra muses about how being able to forget everything would be great, while Rex wonders if Pyra having a body when they found her means her old Driver might still be alive somewhere.

Upon returning to Garfont, Vandham notices that Rex and Pyra have matching wounds from earlier, which baffles him since Blades are supposed to heal quickly and easily. This suggests that if either of them dies, so will the other. Akhos and Obrona then appear, who are swiftly fought off and leave, but they beat down Pyra badly enough that she needs bed rest. Nia wants to talk with Vandham about her past with Torna, but he shrugs her off and says he has no problem with whatever her history or motivations are. He also says he's got a mate in the capital of Uraya, Fonsa Myma, who might know a way across the void around the World Tree.

In the meantime, Jin is aboard a Titan ship, effortlessly slaughtering everyone aboard. He reaches a storage room full of Core Crystals. The ship is then shown collapsing into the sea.

On the way to Fonsa Myma, the party encounters Zeke von Genbu, known as the Bringer of Chaos, also known as The Zekenator, and possibly the Most Evil Driver in Alrest, accompanied by his Blade Pandoria and his mascot Turters. He demands to fight them for control of Pyra, which winds up unresolved due to his comedic incompetence, and he disappears. The party gets to the capital without further incident. Vandham remarks that the military presence is much larger lately, and many think war with Mor Ardain is soon. They come upon a girl being bullied by a soldier for scant rations. Pyra steps in, they beat him up, and he realizes it's the Aegis and runs away. Vandham knows the girl, Iona, as the granddaughter of who he's looking for, Cole. He brings them to the theater he works at, currently playing The Heroic Adventures of Addam. They see the ending, where Addam asks the Architect for power and receives the Aegis, saving the world. Nia elbows Rex into trying to make it less awkward for Pyra, which he utterly fails at.

Cole is in a backstage room, and greets Vandham warmly. Vandham asks about the World Tree, and Cole recognizes Pyra. He says he knows someone who successfully got to the Tree and met the Architect, so he's the one they're looking for. He asks to speak with Pyra privately; he apologizes for the play upsetting her, saying he needs people to know of that time, and is worried about her possibly using the Titan-sinking power again. Pyra also calls him Minoth, a name he'd almost forgotten. He is about to tell the group how to proceed but gets stuck coughing because he's old, so Vandham says to hold it off for today, and they head to an inn. Cole is then visited by Malos and Akhos, the former whom he also knows from ago. Akhos offers to heal him in exchange for presumably where Pyra is, and Cole declines. But Iona is caught watching, and is persuaded to help. Malos appears in Pyra's dream of Elysium, and says to save Iona she needs to meet him alone at the place of her awakening. The rest of the party wakes up to find Iona and Pyra missing. Cole says what happened and that they're probably at Olethro Ruins, so they hurry over.

Malos, Sever, Akhos, Obrona, and Pyra are at the ruins; Iona is there and unconscious. Pyra wonders about Jin, who Malos says he's on the same side of. He then starts to attack her, and she can't really do anything about it, but Rex and the others arrive to make it a fairly even fight. After some time, Obrona then activates an anti-ether field that cuts off the connection between Blades and Drivers, which gives Malos and Akhos a significant advantage over the others. Akhos says Jin wants to use the Aegis's power to wipe all humans from the world. Malos and Pyra disagree over whether "Father" agrees about this being their purpose, and Malos starts to show a greater shadowy power than just what Sever can do. Vandham decides to do a last resort of stabbing himself with Roc's weapons, letting him use the elemental power with his own hands despite the anti-ether field, and fights Malos while yelling at Rex to escape. He is killed, and Roc turns back into his Core Crystal.

Rex angrily rushes at Malos and is easily overcome. In desperation, Pyra seemingly turns into someone else, now yellow and white with long hair and the ability to rain giant lasers from above. Malos refers to her as Mythra and is pleased that he's finally gotten this to happen. Mythra appears to be able to circumvent the anti-ether field, and also grants Rex some Foresight of upcoming enemy movements. In the end, she unleashes a barrage that shatters the cores of Sever and Obrona, killing them. Malos and Akhos bail, and Mythra turns back into Pyra. Rex cries for Vandham.

Chapter 4: Aegis
A flashback plays where dark and light energy rain upon a city and landscape, devastating it to the horror of onlookers. In the distance, there is an unidentified mech and Mythra, both with the same colour and shape of Core Crystal.

The next day, Vandham is buried where he fell. The party pressures Pyra into telling them what happened. Instead, she turns back into Mythra, who chews out Rex for being a dummy and forcing her to wake up to save him. She then reverts to Pyra again to make her explain things, with some extra context from Gramps. Apparently, Malos is also an Aegis, both with enough power to destroy the world. Long ago, a man climbed the World Tree hoping to reach Elysium, and found it empty. To prove his journey, he brought back two Core Crystals, and later awakened Malos from one. This caused a lot of problems, so Mythra was awakened by Addam, hero of the Kingdom of Torna, to try and stop Malos's rampage. They eventually won, but three Titans were destroyed in the crossfire. Mythra then sealed herself as Pyra in a sunken ship to ensure that her destructive power could no longer be used. The two - Pyra and Mythra - would talk in their dreams while sealed, and decided to return to Elysium if ever woken up. Pyra later goes to Rex, and tries to make him feel better by saying Mythra didn't mean to be so angry, given she chose to unseal herself to save him. Rex chooses to instead agree that he was being a dummy, but then turns around to compliment her strength and how she isn't being so closed-in anymore. He wants to protect her in the same way she protected him. Gramps notes this reminds him of Addam, which upsets Pyra.

The party prepares to leave Uraya. Cole gives Rex a dagger and says to take it to Indol, as its owner will reveal how to get to Elysium. He then reveals that he himself is a Blade, real name Minoth, and the dagger is his own weapon, with the subject owner being his Driver. However, he is a Flesh Eater, a Blade having undergone an experimental injection of human cells. Some Flesh Eaters have unique powers, but he is a failure like most, so rather than being ageless he is slowly dying. He wants to see how far Rex gets on his quest, while in exchange Rex asks him to make a play about Vandham.

Somewhere in Indol, a person kneels alone in prayer to the World Tree.

After a detour to Garfont, where Rex is given leadership of the mercenaries at the request of Vandham's last message, the party plans their route to Indol: via Argentum and Mor Ardain. Rex's salvager status lets him travel on Guild ships for free, so they get to Argentum easily, and he gets a discount on the next leg. The party stays at the local inn for the night. Rex wakes up to Mythra in his bed; apparently she sleepwalks, and doesn't take too well to discovering it's happened again. He sees Pyra in the morning, who apologizes. Meanwhile, Mòrag and Brighid have returned to Mor Ardain to meet with the young Emperor Niall and his Blade Aegaeon. Niall wishes to meet with the young salvager and the Aegis, but also informs them of the Core Crystal shipment that Jin intercepted. As a result, the Senate has restarted excavating Judicium, headed by the pro-war faction of Senator Roderich. They may have to deal with that later.

The party is about to embark for Mor Ardain when Rex notices Roc's Core Crystal has started to glow again, and becomes conflicted over whether he should "take" Vandham's partner. He is then victim of a drive-by by some Gormotti kid, who steals the crystal and a whole ship, so they have to take a massive detour to Gormott to chase him down. They find a gang of kids and trained birds using Umon's hangar as a hideout, stealing stuff to get revenge on bandits that destroyed their village. They then hear that since Dughall is gone, the bandits plan to attack Torigoth. Rex gets the kids to tell the city guard for backup, and the party goes to get the bandits. On the way, Roc is summoned to dispel an ether miasma, and he shows curiosity about his previous Driver. They find the bandits and stomp them as the city guard arrives. Rex takes the kids back to Argentum and recommends they work off what they stole, which is accepted.

Everyone finally gets to Mor Ardain, and to the capital of Alba Cavanich. They quickly run into, who was once assistant to Tora's grampypon Soosoo. Tora asks if he knows where his dad Tatazo went, which he doesn't. He does however get them a via-friend discount at an inn. At the hot springs, with Nia, Poppi, and surprisingly Mythra, who insisted to Pyra that she wanted a bath. Mythra spots something unusual about Nia, who asks it remain a secret. Afterward, there are explosions outside, so the party checks it out. Mythra also feels like staying out for a bit, and it's mentioned that she and Pyra share memories. They find that the explosions are being caused by what looks like a robot maid that has taken out military troops - Tora recognizes her as Lila, the Blade his dadapon and grampypon were making. They have a scuffle, but she gets away. Tora decides that, since Lila was not finished when grampypon was shot and dadapon sent him away from the attackers, Tatazo must be somewhere nearby. The military then catches up with them, including Mòrag and Brighid, who mistake Poppi for Lila and so try to subjugate them. Rex uses both Mythra and Pyra in the fight, both of whom hold back, and Mòrag is not thrilled about it. The fight is interrupted by, an intelligence officer who sets the record straight. Mòrag apologizes and suggests they work together to find Lila and whoever is using her.

Tora suggests the party ask around for who's been buying the materials necessary to complete Lila in order to get a lead. They eventually follow the trail to the Old Industrial District, which then leads to an Abandoned Factory elsewhere on the Titan. They go tell Mòrag this and convince her to let them investigate themselves. She replies with rumors that a big-shot Nopon merchant is involved, who Rex assumes to mean Chairman Bana. On the way to the factory, they run into Zeke again, who again tries to fight them and is again expelled from the battlefield by his own mishaps. The player then sees Bana and Muimui overseeing a factory line of artificial Blades; Senator Roderich has been helping them acquire materials, but Bana has no qualms with selling to Torna first, or holding out on Roderich until war breaks out and he's more desperate. The party reaches the factory and sneaks their way in to see the active factory line. Not long after, they spot Tatazo being forced to give production instructions to Tirkin guards. Tora goes in without thinking, and more guards appear alongside Muimui, who says he helped them get here so he could take Poppi's more advanced ether furnace. The party takes out the guards, which spooks Muimui into claming this artificial Blade business is totally legit, but Tatazo says otherwise and has it known that Muimui was even behind grampypon Soosoo's death.

Bana walks in, yells at Muimui, and brags about how much money he'll make when he takes all the party's stuff. He gets confused about Nia being there and spills a bit more information about selling things to Torna, and sends Lila at them. Poppi successfully takes Lila down, but Tatazo gets in the way of the finishing blow because he cares about Lila that much. Lila becomes able to resist Bana's orders, and rips out the override device. Bana and Muimui bail, so the party give chase. The two Nopon enter the cockpit of a giant maid robot called Rosa and begin fighting. Lila grants Poppi the ability to fully-activate her ether furnace, allowing her to transform into an older-looking and more offensive form. Together they disable Rosa, and Bana gets away. They catch up with him at the factory's harbour, and he claims to give up the artifical Blades venture so they don't hand him to the authorities, but Torna has his back - Mikhail and Patroka show up with their Blades Cressidus and Perdido, and they fight hard. Mythra wants to push them over to a specific location so she can use Sacred Arrow, and is aided because Mòrag and Brighid arrive to help. The plan works, and Cressidus and Perdido are killed. Patroka becomes very upset and starts to unleash an angry red aura, but she gets neutralized by a new arrival, someone who Mikhail recognizes as from Indol and thus big enough trouble that they escape onto the hidden Monoceros. Mòrag also recognizes the newcomer as Fan la Norne.

Jin, alone, walks up to a large hunk of ice. A person he calls Lora is inside. She is very similar in appearance to Fan la Norne.

Chapter 5: Masters and Slaves
In a flashback to five hundred years ago, there is a sparring match at Addam's camp. Lora is using Fan as her Blade, though she calls her "Haze", and a hooded man who is presumably Addam is using Mythra. Jin interrupts with food, and a blond child that resembles Mikhail is also present. Brighid arrives during the meal, presumably the Blade of the current emperor of Mor Ardain, and expresses disappointment that she missed the fight. This leads to discussion over how a Driver and Blade are at their strongest when together. It's mentioned how Haze can restrict other Blades' abilities, and how odd it is for her to resemble her Driver Lora so strongly. The meal is interrupted by a report on Malos's plans.

Back in the present, Fan explains she is an envoy of the Indoline Praetorium. Praetor Amalthus is Malos's Driver, and he wishes to see Rex, as he has the other Aegis. Amalthus is also the owner/Driver of Cole's dagger, which implies he's the one that Rex is looking for anyway to try and get to the World Tree. There's some suspicion that this is too good to be true, but they agree, so Fan gets them onto a Titan ship bound for Indol. Mythra catches Fan alone, and determines that she doesn't seem to remember her old life or name. She also notices that half her Core Crystal is missing, nor is it in proper resonance with her Driver Amalthus.

Jin is ruminating on the voices of the Blades he can hear from a wall full of Core Crystals. Malos goes to get him for a Torna meeting: Akhos has found Mor Ardain's excavation in Temperantia, and there are weapons there from the lost Titan of Judicium, where Flesh Eaters were first created. Jin muses over whether to use or destroy them when Mikhail and Patroka arrive. Mikhail says they got the goods but had to run, and he recognized Haze without a doubt. Jin asks about the Marsanes and Mythra, the former being behind schedule and the latter approaching the Leftherian Archipelago. He figures Mythra is going to Indol, and knows that only an Aegis can open the path to the World Tree, so he goes to Temperantia to buy some time.

The party's ship reaches the Leftherian Archipelago. The Cloud Sea forms a massive ridge here, which is easier to go through (via the Leftherian Titans) than around, so they disembark. Rex is excited to be back after five years, so Pyra suggests they stop by his hometown of Fonsett Village. Nia asks why Mòrag is still hanging around, the answer being she's representing Mor Ardain in whatever business Amalthus has with Rex. The group gets through the tunnel through the ridge without incident, and witness some kids diving into the clouds.

A man who is presumably Senator Roderich is in Temperantia, taking stock of the Judicium excavation. He doesn't seem too impressed with proceedings, mostly for personal reasons.

Rex is mobbed by old friends as he returns to Fonsett, and Aunt Corinne is not far behind. He leaves the party to hang around the village while he goes for a walk, taking Pyra to his parents' graves so she can "meet" them. Pyra later speaks to Corinne after a meal, who first teases her, but then tells Rex's story: his mother arrived with him when he was two and died straightaway, and his father was found dead not long after. Pyra seems to reconsider staying with him, so he won't suffer any extra, as she thinks that nobody needs her. Brighid is eavesdropping.

The party continues to Ysheva Harbor, where they find that Zeke has been waiting for them. The party tries to just push him aside again, but he turns out to be an actual threat this time. Mòrag steps aside, since Zeke is the Crown Prince of Tantal, and she doesn't want to cause a diplomatic incident. The rest of the party fights him, and eventually come to a mutual standoff, with Rex holding back because he decides Zeke isn't a bad guy. Zeke is satisfied, and explains his deal: he's been looking for the Aegis as an envoy for Indol, and says Rex passed his test. He then falls into the Cloud Sea again, although he reappears shortly.

The next ship the party boards takes them directly to Indol. They wander around to kill some time, and find a bunch of refugees protesting the use of Blades, since Indol has a monopoly on Core Crystal distribution. Pyra also asks Mòrag why she's just letting Rex do what Mythra wants, given she was trying to stop that earlier, and she answers that she doesn't want to see Rex under anyone's control. Zeke implies it's something else, and she rebukes him. Fan shows the group to their rooms for the night. Rex asks Pyra about Addam, and she answers that Mythra sees him as a good person very much like Rex. Rex is embarrassed by this comparison. The next morning, Rex runs into Fan staring sadly at a mural, and Nia teases him about having a crsuh on her. Fan says that the mural, the creation of Alrest, makes her think about where her memories have gone. Rex suggests asking Mythra, which is an appreciated idea. Brighid and Pyra are also talking about long ago, where Brighid reveals she keeps a journal of all her previous incarnations, so she can keep a record of what she forgets when reborn. Many Blades try to do this, but often fail because their inactive Core Crystal is easily separated from their journal, but Brighid is a well-protected imperial treasure. Brighid also says that she suspects what Pyra truly wants, and that she ought to tell Rex everything if she really trusts him.

In a flashback, a man recognizable from Cole's story of the past looks at the mural of the creation of Alrest. He returns to his room to consider his plans. The flashback continues to his journey up the World Tree, entry to the unseen Elysium, and hastened escape with the two Aegis crystals. He returns to Indol, considers the crystals, and reaches for Malos'. Thus, this man is Amalthus. In the present day, Amalthus is waiting for Rex and his group, and they arrive shortly. He says he considers Rex equal to himself, both being Aegis Drivers. Rex offers Cole's dagger, and asks for help to get to Elysium. Amalthus answers more harshly, channeling Malos, and says he did not find Elysium up the World Tree because he was "unworthy". That said, he does pledge his help, and asks for a moment alone with Pyra. Rex is unnerved by having felt Malos, but he can't tell if it's real. Amalthus takes Pyra to the mural and wonders whether people have progressed or regressed. Mythra appears and comments on how Amalthus has not changed in five hundred years, and doesn't believe that just his race and being an Aegis Driver is enough of a reason. She also wonders why he's changed his mind to letting people try getting to the World Tree, and he flips it back on her to ask whether she felt Rex would be good enough to resonate with. The meeting is over, and Fan suggests the group stay another night. Mòrag and Brighid hear that Senator Roderich was secretly in Indol this night, and suspect he's making behind-the-back deals with the Praetorium.

Jin appears in Temperantia. He gets into the Mor Ardain regiment, activates one of the excavated Titan weapons, and drives it through the demilitarized zone to attack the Urayan regiment. The party is called to the Audience Chamber as soon as the news breaks. Mòrag is very upset that someone declared war without the emperor's approval, so she goes to find out, and the party is asked to follow. Mòrag finds Roderich immediately, who is also yelling at people trying to figure out what's happened. They figure out that the only people that gain anything from a war at this point are Jin and Torna, and decide to go try and stop it. Fan asks to come along, since her neutralization power works against Titans as well, so she thinks she can help. Zeke also stays because of what he's heard about Torna.

The group approaches Temperantia. Mòrag orders the ship docked in front of the rogue Titan weapon so they can head it off. They find it amongst a bunch of Urayan wreckage. Mòrag tells the group how to disable it without accidentally blowing it up. Fan uses her power to halt the Titan under a cliff so they can all jump on, and they take out the power lines. Jin comes out to meet them. Fan tries to be mighty and arrest him, but he offseats her by insulting her lack of memories. Mythra asks why he's switched sides, and he only says he realized Malos was right, which she doesn't believe. Rex realizes that Jin is a Blade while Jin and Mythra yell at each other, with Jin blaming her for presumably Lora's death. Jin then removes his mask to reveal a blood-red Core Crystal in his forehead. Fan tells him to give up because she can shut him down, and Rex makes the connection that Patroka is probably also a Blade. They have a fight, and since Jin is apparently one of the most powerful Blades in history, he isn't completely helpless against Fan's abilities. He teleports forward and stabs her core, saying he's done her a favour. She moves as if she agrees, but Jin suddenly thinks of Lora, and he jerks away. He explains to Rex that Blades losing their memories on death makes them so much less than humans, despite being the superior species, and that Indol controlling all Core Crystals makes all Blades slaves to them. He then starts to ready something big, but falters. The party can't capitalize because Akhos appears and uses leftover energy to reactivate the Titan weapon, so they have to break the local defences as Torna gets away. Rex is upset that despite being a Driver he wasn't able to save Fan, who suspiciously still has a body.

The armies of Uraya and Mor Ardain begin to arrive and charge weapons, causing Mòrag to furiously curse on who gave the order to attack Uraya. They are interrupted by Indol itself standing between them.

Chapter 6: Wounds
In a flashback, a child awakens Jin. A man is incensed about this, since he stole the Core Crystal fair and square, so he decides to kill the child to send Jin back. A woman tries and fails to stop him, so Jin does. He vows to keep the child safe, and she says her name is Lora. In the present, Jin awakes from healing. Malos tells him to stop risking himself, but also wonders whether the two of them are really themselves, or someone else.

The rulers of Uraya, Queen Raqura, and Mor Ardain, Emperor Niall, meet in Indol for an emergency tribunal. Also present are Mòrag, Brighid, Zeke, and Niranira, now Acting Chairman for Argentum. Meanwhile, Mikhail, Patroka, And Akhos are sneaking around outside, wanting to do some easy assassinating but having to wait because the path to the World Tree isn't open yet and Jin needs it to be opened in order to kill the Architect. Raqura complains that Indol isn't supposed to interfere in war by treaty, and begins by accusing Mor Ardain of breaching the neutral zone. Zeke explains that it was Torna that did it, not any authority of Mor Ardain, which Raqura doesn't believe until Niranira corroborates. Amalthus also says that Malos is involved, which is also disbelieved until Mythra enters the room to confirm it. Mythra says that Malos seems to not have completely recovered from his battle with her, so he wants to reach Elysium, where he can fully heal in order to wipe out humanity. Amalthus says this is why he blocked all passage to the World Tree since the Aegis War, but this clearly does not apply to Malos, so the time may be now to open the way.

The next day, the party, minus Mòrag attends Fan's state funeral. Nia teases Mythra for keeping distance from Rex, but then asks why Fan just died instead of reverting, and Mythra suspects it's related to half her core being missing - or perhaps stolen. After, the party goes to see Amalthus, and find him performing a cleansing ceremony on a group of Core Crystals, making it easier for them to resonate properly. He says he can do this because he is an Aegis Driver, so Rex may or may not be able to do similar. Amalthus then explains that the Great Void around the World Tree is carved by Ophion, an Artifice of the Aegis. It died in the Aegis War, but then the people of Tantal revived it, and told it to keep all away from the World Tree by creating the Great Void. To stop this, the party must go to Tantal, and find the Omega Fetter, the only thing that can undo Ophion's orders. As a result, Torna will be searching for it as well, so Amalthus asks them to get there first. Later, Zeke explains that the people of Tantal are descendants of the Kingdom of Torna, Addam in particular. There is a flashback to not long ago when Mythra asked Amalthus about awakening Haze, him saying that her power was of great use to him in repelling attacks from Torna, though she suspects something is amiss since he has no other Blades. He also says that Torna took the name of the country because Jin was a Blade from there.

The party passes by many tense soldiers of Uraya and Mor Ardain as they head to port, as another summit is to be soon, without Indol present. Mòrag is elsewhere discussing with Niall what he wishes to do; he thinks Uraya won't take anything less than shared ownership of Gormott, which would be a painful process. Niranira then busts in with an emergency: Bana is planning to assassinate someone at the next summit, and several giant weapons are being built at his old factory, with one unaccounted for. Mòrag decides to ask the party for help getting this handled without it leaking to the public. With some asking around, they deduce that he is planning to poison the banquet, so they get onboard the ship where it is to be held. They find a bunch of Tirkin preparing the meals, so knowing that Bana's used Tirkin as henchmen before, they attack. Pupunin appears afterward and says they're a world-famous band of gourmet chefs, so Pupunin angerly demaned conpensation from them.

There is then an explosion in the hangar, revealing that a very large and very suspicious create has been hiding Giga Rosa, an upgraded Rosa that Bana is piloting. The party defeats it again, and Bana is ousted, so he readies a self-destruct. Niall and Aegaeon have a miscommunication; Aegaeon raises a shield around everyone, but Niall runs out of it to try and stop Bana, and he is fatally wounded in the explosion. Raqura is moved, while Mòrag is distraught, and Aegaeon vanishes. Nia demands that Dromarch cause a distraction, which is awkward and successful, and everyone else leaves the hangar. Nia approaches Niall and assumes a new appearance, with a mottled blue-and-red crystal in her chest, and successfully revives him. Everyone re-enters to find Niall alive and alright; Nia is back to normal and tries to play off his injuries as trivial. Not long after, Niall is bemoaning now much paperwork he has to do. He orders Mòrag to stay with and protect the Aegis as his emissary. Mòrag balks because she needs to protect Niall more, but he knows she has Rex's interests in mind, and he gives her Aegaeon's core because he seems himself as having failed as a Driver. They reminisce about the peaceful past, and how Mòrag would have been empress if not for him being of a more direct line, they refer to each other as siblings, but are actually cousins. Mòrag accepts his request, and rejoins Rex. Raqura returns home, realizing that the Aegis' reawakening has changed matters.

The party boards a ship to Tantal. Zeke asks Rex whether he likes Pyra or Mythra better, and they banter about that for a bit. Rex then asks why the prince of Tantal was in Indol, and it comes out from Pandoria that he was disowned because he liked to travel rather than be useful, because of how isolationist Tantal is. He was found half-dead by Indol, so he started living there. They then reach the location of Genbu, Tantal's Titan, which is coaxed out from under the clouds by Pandoria. The king is aware that their Titan is surfacing, and that Amalthus has met the Aegis and is making a move, so he knows he must act. The group travels through the snowy fields, and Nia notices the Titan's ether lines seem oddly dim, which Zeke says is because Genbu has bad circulation, and causes the cold climate. On reaching the capital of Theosoir, Zeke also points out that all the normal shops are closed because there's not enough local food to sell, so only the black markets are thriving.

Zeke brings the group to King Eulogimenos, and Rex gives him the message from Amalthus. He rips it up, sets the guards on everyone, and uses a machine to capture Pyra. The party is sent to jail, while Zeke follows Eulogimenos to a chamber of riches to try and get some answers, and gets nothing. Rex wastes some time trying to break out of the group's cell, but the room is built like a large ether net, so nothing can be done - except for Poppi, since she makes her own internal ether energy. With some modifications, energy stored from Mòrag's earlier suspicions, and Rex learning that Blades can simply make new copies of their weapons, they break the door and escape. Zeke crosses paths with them and directs them underground, where Pyra has woken up to find she has an ether accelerator pointed at her. Eulogimenos arrives and says it isn't personal, but he has to destroy her to save the world. The party arrives and starts fighting through the guards, but the canon finishes charging before they get anywhere. Poppi is deployed to lift the cannon so it misses its shot, and Zeke rescues Pyra. Eulogimenos reveals that the people of Tantal are not actually descendants of Addam, and only became relevant in the post-war confusion, claiming importance to try and keep the people of Torna united. Pyra says that Addam foresaw that this would happen, so he chose to not return to them, and left them a holographic message in her earring: he wants the Aegis to return to humanity after they learn to live better lives. Eulogimenos is shook.

Genbu suddenly breaks free of the Omega Fetter's control, caused by firing the ether accelerator, and is diving deep into the Cloud Sea. Zeke starts to make evacuation plans, but Pyra thinks she can fix the Omega Fetter, so the party agrees to head there. Eulogimenos is surprised that they're willing to do this even though he tried to kill Pyra. The party proceeds onward, though Mòrag suspects something else is between Tantal and Indol for the king to be so upset. They get to an old battleground of the Aegis War, where several Artifices fought, including Siren (Mythra's that shoots the light beams from above). According to Pyra, Artifices are divine weapons from Elysium, which she can't understand because she remembers nothing about it.

The party reaches the ancient building that houses the Omega Fetter. Pandoria opens the door, and they enter to see a golden sphere, which Zeke opens to reveal an angry red crystal. Mythra focuses on it, and it is restored to a blue cube. Pandoria gets Genbu to start surfacing again and tells Rex to take the Fetter with them. The group leaves to find Akhos, Mikhail, and Patroka, all of whom are Blades and Flesh Eaters. They are beaten, but Jin arrives and stabs Zeke, though not fatally, with Jin complimenting him that he isn't called "Thunderbolt Zeke" for nothing. Malos is also now present, though he insists on just watching. Jin reveals his true form, mostly fancy black armour, and has a fairly easy time taking everyone down with his control over "elementary particles", letting him move at the speed of light and be simply immune to Mythra's blasts from Siren. He breaks the Aegis sword as the party is also attacked by a swarm of Artificial Blades. Pyra decides to give in, and threatens to kill herself using Siren's targeting ray, rather than the actual cannon if Jin doesn't pull away. Jin is surprised, but agrees. Pyra takes the Omega Fetter from Rex and goes with Torna as they all leave.

Chapter 7: The Fear She Carries
A very old man gazes upon three empty hollows in a panel, all in the shape of Aegis Core Crystals. Amalthus recalls when he awakened Malos. He hears the news that Jin has the Aegis, so Rex must've been pretty worthless, and instructs his aide Hector to prepare a ceremony.

Rex wakes up in a room in Tantal after two days, still with the handle of Mythra's sword. He decides to give up, to go back to Argentum and start salvaging for work again, and comes out to let the party know. The party pile on him for this, and at least put a dent in his decision before the king sends for him. Eulogimenos gives his apologies and explains that the kingdom of Torna was split long ago - Addam's camp wanted to live with Blades and Titans as equals, while others saw them as tools and themselves as masters. When Addam vanished, his opponents took power, and Tantal was formed. Indol kept quiet about all this in exchange for an annual tribute of Core Chips formed from the ether of Genbu - it is the Core Chip siphoning that causes Tantal to be so cold and desolate. Eulogimenos now understands that the Praetorium did this as part of expanding its influence in the post-war chaos. But he, and others before him are too afraid to change this, to rejoin other societies and expose the truth that they are not truly Addam's descendants. In fact, the letter from Indol was a threat to expose this if they did not hand over the Omega Fetter, so he chose to try and fight back against them, and accepts that he may have made things worse. Eulogimenos also presents a book, mentioning the white and red swords of Addam, and says that the author was looking for something after Addam vanished: the third Aegis sword. Supposedly, this third sword was too powerful for Addam to use, so he sealed it away somewhere. Thus, Eulogimenos believes that Jin only defeated Rex because he lacked this true power. Rex gains new vigour, and decides he needs to find the third sword. Eulogimenos says the author suspects it is in Leftheria. Gramps says he knows the way. Eulogimenos also tells Zeke to stick with Rex, which was the plan anyway.

Malos and Akhos have Pyra in front of Lora's body. Malos suspects that the reason Pyra gave Rex half her Core Crystal was to replace his heart after Jin stabbed it, since Aegis crystals contain the information to replicate all life-forms, and was going to transfer the rest of her core to Rex before killing herself had Jin not agreed to back off.

In Fonsett, Gramps explains that Addam founded the village after his travels, and it was also called Hero's Rest. Addam had charged him with protecting the village, and specifically the secret of the Village Guardian, a statue in the shape of the Aegis crystal. Gramps shows him where to find an Addam's Crest, which moves the statue into the ground and opens a passage. It leads to the Spirit Crucible Elpys, a cavern inside the biggest Leftherian Titan, covered by the cloud ridge. Addam hid something there long ago, presumably the third Aegis sword.

Malos has brought Pyra to a ruin within the Great Void, recalling how much damage she had done to him long ago, and taking off the plate that conceals his still-broken Core Crystal. Akhos and Patroka are elsewhere, discussing how Malos is the Master Blade, and he'll be able to restore himself using what he's missing from Pyra's core.

The party enters the Crucible, which begins to sap the strength of the Blades, both due to a lack of ambient ether and ether-absorbing safety measures. Gramps says there's a chance they may be forcibly returned to their cores and never reawaken. Poppi is immune to all this, so she'll be fine. Zeke and Pandoria immediately get into an argument over who should stay or go. As they go deeper, the truth comes out: Zeke has part of Pandoria's Core Crystal in his chest, making him a Blade Eater - the opposite of a Flesh Eater. Pandoria was so desperate to save his life that when Amalthus found Zeke dying, he chose to split her crystal to save him. Nia feels conflicted over how easily Zeke admitted it, while she suffers in silence. Part of the path ahead looks broken into, so Gramps thinks that the Torna gang might've been here earlier, before realizing they needed Pyra and going to search for the ship she was asleep in. Rex notices that Nia is having trouble, so he offers a salvagers' air bottle. She feels better enough to answer Rex's moaning about his salvager buddies not being real parents, by saying her father was a Gormotti lord that did nothing much but teach her how to be a proper lady. She also says she had a sister, who was always sick. Her father spent so much money on trying to cure her sister that he was no longer a lord, and their lifestyle after that essentially killed her.

The group gets to a blocked pathway. The Core Crystal segment on Rex's chest glows, the obstacle retreats, and they continue through many more ruins. Nia begins to think more about her family, how her sister's life was now tied to hers, how she was taught to call her father by that name, and how she found Dromarch's crystal after he died. She continues her story to Rex, how she had to keep running from Indol, and eventually met Jin and joined Torna. Rex can sense something's bothering her, and tries to encourage her to let it out. The party reaches the Vault of Heroes, which seems to be a dead end, and are attacked by innumerable shadows that take the form of Addam with Mythra's sword. With Rex having trouble as the fight drags on, Nia has enough - she reveals her true form, a Flesh Eater Blade, and grants Rex her weapon, the Catalyst. She also confesses her love to him, which he shrugs off. Eventually, the Addam shadows acknowledge that Rex fights for someone other than himself, and all vanish. Rex then finds himself and Addam under the tree in Elysium where he first met Pyra. He asks Rex what he wants, to which the answer is the power to protect others. He then says that Pyra/Mythra is afraid to accept herself, and taking on their weight is how Rex will become her true Driver. Back in the vault, Rex approaches a stone tablet, which falls away to reveal the third Aegis sword. Rex takes it, and sees an odd vision: a planet, the three hollows, and the very old man. The sword then fades away, which upsets everyone else, but Rex knows it's fine - they just have someone to rescue.

After getting back to Fonsett, Rex says that he now know Pyra is in a rotting Titan near the World Tree. Mòrag believes her is referring to the Cliffs of Morytha, a long-dead Titan stuck in the side of the Great Void, and has a military vessel take them there. Meanwhile, Mikhail is readying the Marsanes, the last battleship of the Kingdom of Torna, for battle with "non-mortal" opponents. Also, Malos is busy paging through Pyra's memories while picking out the bits that will restore him and trashing the rest, which Rex can feel is trouble. Malos then finds something impressive, which he likes to see. Jin is also busy is his own thoughts, recalling memories of Lora, when Malos finishes and steps up to him. He says Pyra is just a "lump of meat" now, and he just has to wait for Mikhail to finish his work before they can continue. He then uses the Omega Fetter to summon Ophion, who immediately tries to shoot him because it has its own instincts, so he goes to fight it.

The party gets to Malos at the Balquors Ruins, his Core Crystal visible and whole. He says they'll never see Pyra again, and uses his own sword to blow a hole in the ground around them. Zeke tries to attack, but he strikes a shield and his sword is partially disintegrated. Nia says Malos's power can destroy anything it touches, but she has the power of mass regeneration, which can counter it. They do battle, and Nia inverts her power on Malos, giving him some sort of cancer and causing him to stumble off the cliff. The party moves on to find Jin and Pyra, and Malos reappears from behind them, alive and well. Malos brags about having removed all of Pyra's memories, and chucks her inert body at him. Rex makes a speech about how he was wrong all along but now understands what he has to do, and Jin silently realizes something, Rex asked everyone stand with him one more time, as they prepare to engage Jin and Malos. Despite their best efforts, Jin uses his ice powers to reduce Nia's healing abilities. Rex starts to hear Pyra and Mythra's voices telling him to give up, because they only wanted to go to Elysium so they could ask the Architect to let them die, but Rex refuses, and demands they rejoin him. He suddenly finds himself in front of the two of them and the huge machine that Malos saw, and they all agree to continue on. In the real world, the third Aegis sword appears in Rex's hands, and Pyra revives and transforms into a matching third form, Pneuma. She gives him a new outfit to match her own. Now, Rex can match Jin's speed, and they give him a beating while choosing to not kill him, but not before noticing sadness in Jin's eyes. Malos says he was created as the ultimate weapon to destroy the world, so he's going to Elysium to awaken the Artifice Aion, but for now settles for having Ophion attack them. It fails because it was shot by Siren, now present rather than distant, and the Artifices fight. In the crossfire, the cliff everyone is standing on is destroyed.

Chapter 8: World Tree
Pyra and Mythra talk with each other in their Elysium dream about how the bell has finally stopped. In the real world, Mythra wakes up beside Rex in what looks like a destroyed cityscape, a legendary place under the Cloud Sea that salvagers call the Land of Morytha. Rex sees the World Tree's roots in the distance, and they start to look for everyone else. Mythra explains that the third sword lets her control Artifices at will, and that her Pneuma form is both Pyra and Mythra at once, rather than either individually. Rex decides at this point whether to call the third form "Pyra" or "Mythra"; this page will continue to use "Pneuma" for clarity.

The two find Jin being attacked by a humanoid monster. Rex decides to help; Mythra hates the idea but follows. They take down the Guldo monster, but it revives; Brighid arrives with Poppi and Gramps, and says they have to be incinerated or have their Core Crystal smashed to actually destroy them. Rex asks Pneuma to heal Jin, and she reluctantly does, as the Master Blade contains data for all Blade cores. By doing this, she discovers that Jin has a human heart, making him a Flesh Eater; Mythra suspects it's Lora's heart. Rex tells Jin he's not going to kill him here, but he'll keep standing against him if necessary. Jin says this place was the Architect's birthplace, destroyed long before the creation of Alrest. Still weak, he agrees to join the group until they can leave the area and reach the World Tree. In addition, Brighid temporarily attaches to Rex, which can be done as he is the Master Driver.

After travelling a distance, the group takes a break. Brighid challenges Jin as to whether what she wrote in her journal of the past he knows is true. Jin counters by saying he's talking to an entirely different Brighid, but a Poppi interruption prompts a memory of when Lora was officially made a Driver of Torna. Later, Poppi steps away to look at the buildings, and wonders how more advanced and thus happy the people that built them must have been. Mythra is more sour about these ideas, which leads to discussion over them being created with power that may or may not destroy the world. They attempt to make a promise together, but Mythra backs out and reconsiders, though Poppi demands they keep what they have of "Mythra will stop Poppi from destroying the world".

The Monoceros dives deep into the Cloud Sea and comes out in the Land of Morytha to search for Jin. Seeing the ruins, Mikhail starts to get cold feet about Jin's plans.

The party finds the remnants of the Titan of Torna, and decide to investigate. They quickly find a cavern filled with what looks like Titan-like Blades in large eggs, which Jin says are Blades that died while becoming Titans. Blades are not truly immortal; once they reach the end of their life cycle, they return to their original Titan, and attempt to metamorphose into Titans themselves, with no memories of being a Blade. They continue inside to see more Titan-reverent architecture; it was the sacred foundation of Torna for humans, Blades, and Titans to live in harmony. Recalling this, Jin says that not long after Addam vanished, Amalthus attacked Torna, fatally wounding Lora. With Lora lamenting how being forgotten is worse than death, Jin decides to eat her heart so he can persist, and she agrees to it. Amalthus was afraid of the Aegis, so he attacked Torna to try and capture or kill her, but with Addam having sealed her already and vanished himself, all he did was erase the remnants of Torna. This turned Jin into always assuming the worst of humans. In fact, Amalthus was to use the Architect's power to erase Blades and Titans, so only humans remain. Rex declares that this makes Amalthus and Jin's group equally bad, though he thinks he doesn't truly want to kill the Architect, because he sees the same "I want to die" look in his face that Pyra once did. Jin stands firm, saying he and his Blades are sick of being used as tools by humans.

The discussion is interrupted by a large Guldo, which Jin now says are destructive cybernetic organisms. The missing half of the party also arrive to help, and it is eventually defeated. Rex finds it dropped what appears to be a human ID card. The party steps outside to decide what to do next when the Monoceros arrives. Jin orders them not to attack, and as he gets on the ship and leaves, he says Brighid is as she used to be. Rex realizes that Gramps knew everything about Jin from the start, which he says he kept hidden because Rex is too caring. The party begins to travel along a root towards the World Tree's trunk. In Mor Ardain, Niall receives news on how warm the Titan's ether is getting as it continues to age, with a suggestion to hurry up and move the capital to Gormott. He rejects this, and knows Gormott is also already in decline.

The Great Void is filling in, with Ophion no longer maintaining it. The group enters the trunk of the World Tree to find it is mostly mechanical and there is an elevator in the middle, so they get in and go up. Meanwhile, Jin is recovering again aboard the Marsanes, and tells Malos he found the Torna Titan in Morytha. He seems less sure of himself, but Lora's body is still there, to remind him to not trust the Architect. The party ascends the inside of the World Tree, seemingly a large and complex building. Rex starts to think about how Amalthus must also hate humans as well as Blades and Titans, while Mòrag suggests that he attacked Torna to intentionally reduce the number of new Titans so Indol could keep a stronger hold on things. Rex concludes that Amalthus probably hates everything and wants to destroy it all, much like Malos. A flashback is then shown of a very young Amalthus being pushed off a cliff by his mother, who he later finds chased and killed by bandits, and he kills the bandits. In the present, Indol rises up near the World Tree to find the Marsanes, and they begin to fight each other.

Nia asks the other Blades in the group how they feel about living beyond their Driver's death, and they all say they aren't interested. She remarks how, as a Flesh Eater, she doesn't need humans. But Jin was collecting Core Crystals, yet not using them to make more Flesh Eaters, not expanding Torna's ranks against the humans - in fact, he was against Akhos resonating with Obrona. So, she thinks he feels the same way. The group then gets to an exterior portion to see the fight between Indol and the Marsanes. Amalthus recalls seeing Malos's power for the first time long ago. Malos later left him, not needing a Driver to stay alive anymore, and that he would finish what Amalthus supposedly started by wiping out the worthless humans. Amalthus had hoped that someone out there could use the other Aegis against Malos. In the present, he sends some Indoline monks to order Rex to use the Aegis to bring down the Marsanes, which is refused. In response the monks attack them but were defeated swiftly, Amalthus then reveals that he indeed took the other half of Haze's Core Crystal, and extends its Blade-neutralizing power across the party. He also hijacks Mythra's control of Siren to strike the Marsanes, proclaiming himself as the Master Driver of the Aegis, he has the power to control all Blades and Titans. Malos tells his crew that they're fine, since Flesh Eaters, though their powers dampen and their army of Artificial Blades can't be controlled.

The Marsanes reaches what they call a "boundary layer" that Titans and Alrest ships alike cannot cross, so they approach the World Tree to offload Jin and Malos. Rex tries to tell Amalthus that he's going to stop them, but Amalthus is going to destroy them himself since he doesn't think just talk will do any good, and supposedly only he knows the true will of the Architect. Rex uses his own Master Driver ability to wrest back control of Mythra. In response, Amalthus summons Mor Ardain who arises and fires a weapon of its own.

Chapter 9: Rain
In a flashback, Amalthus pays respects to many dead soldiers and helps the needy in his travels for Indol. But he finds a man he aided committing burglary and murder, entrenching his view that humans are beyond help.

In the present, Mor Ardain's attack, ordered by Amalthus rather than its people, struck the World Tree rather near the party. Gramps says that another shot might waste enough energy to cause the Titan to collapse. The second shot hits the Marsanes as Uraya also approaches and fires its own attack. Mikhail tells Akhos and Patroka to get out and follow the other two, and they do. He then converts the Marsanes into a humanoid form, and goes to punch Indol in the face. Amalthus assumes that Mikhail is a Flesh Eater, but he's actually a Blade Eater, so he can't be controlled or suppressed. In fact, he's one of the refugees that Amalthus experimented the procedure on. He keeps giving Indol the beatdown when Tantal arrives. This is all getting very out of hand; Rex has a guess that the pillars on Indol are amplifying Amalthus's ability to control the Titans, and that smashing the pillars will weaken or end this ability. Mythra can't get a clear shot, so Pyra suggest they move closer, which can only be done if they both hitch a ride on Poppi. Amalthus spies the trio approaching and realizes they know what to do, but can't stop them, and the plan is successful. The Titans stop their aggression. Enraged, Amalthus gets a shot from Indol towards the party, but Mikhail gets the Marsanes to block it. He doesn't really know why he decided to this, aside from a longing for his own friends from long ago. He directs the Marsanes at Indol once more, which is preparing its ultimate attack, and gets in the way point-blank. Mikhail sacrifices himself by detonating Marsanes, and Indol falls into the Cloud Sea.

The party continues up the World Tree. Zeke recalls how he once spoke to Amalthus as an envoy, stating his view that killing another person means you are weak, and Amalthus responded by saying he hated this world. As a result, Zeke asks Rex if he likes this world. He answers that there's good and bad in the world and its people, and that's alright - and he likes himself, too. Zeke suggests what might happen if someone who hates himself - Amalthus - were to meet the Architect. Jin and Malos are ahead, and Jin is preoccupied. He decides he will stay here while Malos proceeds to their goal, which irks Malos but he goes with it. Jin recalls the time when someone who knew one of his previous lives directed him to a previous house, finding pictures of and messages from a him he doesn't remember, including how to become a Flesh Eater. Then, the party arrives. It's unclear whether he truly wants to fight, but he told Malos he will, so he does. Jin is convinced that if Rex opens Elysium to humans, they'll just turn it into another Morytha, as they did to Torna, since Rex can't live forever to stop them. Rex says that's what Blades are for - just like humans, Blades' past selves are passed down to new selves. In fact, he's envious of Blades turning into Titans to provide land and making many new Blades. So, he needs to ask the Architect why everyone was created, if only to confirm that his guess is right. This is enough to convince Jin to stop fighting, but he's weakened from the battle and his limitations as a Flesh Eater, and falls to his knees.

Akhos and Patroka arrive to save Jin. Patroka asks Nia to heal him, but she is then attacked by a strange being that turns out to be a heavily mutated Amalthus, and he crushes her core to add it to those in his armour, killing her in the process. He rambles on why the Architect sent the Blades in Alrest, claiming it was for his sake to enable his cleansing procedure, in which he extracted the data from all of the cores he cleansed. He remains convinced that the Aegises are only to destroy, which he knows because he believes that he is an agent of the Architect's will; Dromarch and Pandoria rebuke his claims. Pneuma realizes that Amalthus's worldview is what caused Malos to be the same way. Akhos recalls how Jin saved him and Patroka once - not themselves siblings, but the flesh of their Drivers were. He tries to attack Amalthus, only for him to grabs Akhos, chastising him for being a mere Blade who very existence depends on how long the Driver lives. Rex and the rest of the party tried to save him but to no avail, with Zeke telling him that they are all friends with the Blades. Amalthus is angered by the concept, and in retaliation, he kills Akhos by tearing out his Core Crystal. Before dying, Akhos remarks that it was painful, and if he was still a Blade it wouldn't happen to him. Amalthus then fights the rest of the group. Despite being defeated, he refuses to give up, and as a last ditch effort, fuses with the World Tree in an attempt to destroy it from within. Jin helps them out, and now believes that Rex should stop Malos. He uses the last of his power to deep-freeze Amalthus, killing him. As Amalthus is dying, he is greeted by a vision of his mother. With his power used up, Jin's Core Crystal shatters and he dies, with his body vanishing. In a flashback in an unknown town, Malos finds an abandoned Jin, and remarks the living conditions in the town. He introduces himself, saying that's he the same as Jin and then offer his hand to him.

Chapter 10: And thus, boy met girl.
In the year 20XX, there is a battle being fought in near-Earth orbit, near the First Low Orbit Station called Rhadamanthus and its space elevator, the Beanstalk. The enemy are known as Saviorite rebels, and they are winning against the station's Siren units. The order is made to activate the "Conduit" in order to release Aion, but a Professor Klaus has locked it out so he can begin an "experiment" and birth a new universe. His colleague Galea attempts to stop and dissuade him, but he is convinced that the Conduit's power will open a gateway to a new world and allow humanity to move past their mistakes, and they must at least try it rather than surrendering the station. He begins the procedure, and a pulse of light surrounds the planet.

In the present, the party has reached high enough that stars are visible outside, and Rex hears the bell of Elysium. Meanwhile, Malos has reached the old man who is presumably the Architect, who calls Malos "Logos". Malos tries to kill him, but nothing happens and tells him that's he's dying anyway, so he moves on to his question: is the choice of his role really his? The Architect responds that it was both him and Amalthus, which Malos accepts, and leaves to control of Aion, but not before thanking him for creating him. Rex leads the party to where he believes Elysium is, and they find it - an empty wasteland, some buildings intact and all life long gone. Rex and Pyra are both distraught, but agree to investigate the bell coming from the church. The bell stops when they approach, and they hear the Architect's voice inside, directing them into a secret passage that leads back into the metallic constructions of the World Tree. Rex blinks, and everyone vanishes. He then finds himself in a series of unnerving dreamlike locations, including out-of-character recreations of the other party members that try to break his resolve. The experience ends in Fonsett, which seems much more real to start with, but both Pyra and Mythra are there and they have each others' personalities, which at this point is unsettling enough to cause Rex to break down. The charade ends, and everyone appears in a dark room.

The Architect is pleased, revealing himself and saying his name is Klaus. He knows everything they have done and thought, and sent them these visions now to see their fears and measure how mankind has changed. He explains the scene of 20XX in simple and vague terms, that he opened the Conduit hoping it would change the world for the better. Instead, many parts of the world fell through the Conduit to distant universes, with only the ruins of Morytha and half of his body remaining. The other half of his body lives elsewhere, though not for much longer, explaining that his other half's death is approaching. He viewed this as punishment for what he did, so he vowed to restore this world. He began with the Cloud Sea, a substance that can restore deteriorated matter, so bit by bit the world could be rebuilt. From there, he recreated life in the form of Core Crystals, vessels with memories of former lifeforms. The crystals combined with the sea to form the ancestors of Titans, and from there a new form of mankind evolved. Finally, he guarded against the chance that someone like him would later appear by creating Blades, overseen by the three Aegises: Ontos, Logos, and Pneuma. The Blades would transmit information about the state of the world to the Aegises, and the Aegises would send back new, further-evolved Blades and Titans. The Aegises were formed from what was once the space station's Trinity Processor, but Ontos triggered a space-time transition event and vanished, so only Logos and Pneuma were left. It is also revealed that the Guldos in Morytha are the survivors of the previous world, mutated by the first Core Crystal prototypes that were planned to replace human brains.

Despite all this, the Architect allowed Amalthus and Malos to run rampant. He believed such things are fate, and that the impending failure was his from the start, but what Rex has done has changed his mind. However, Malos is now beginning to try and destroy the world, the Architect reminds the party that at heart, Malos is just an information processing program, neither good nor evil, as he knows nothing but Amalthus's despair. The Architect then asks Rex what he wants, which is just to stop Malos (and maybe try to be friends with him later). The Architect gives Pneuma ultimate control over all of Elysium, and warns that when he disappears, so will the Conduit and thus Pneuma's and Rex's powers. As the party leaves, Rex ask the Architect if he changed his mind about the world, which he replies to him that he was glad that he met them, and then thanks the Architect for creating life. The Architect then muses that he and Galea will see each other again.

Pneuma leads the party to Aion, the Artifice designed only to destroy the world, as multiple Sirens and Gargoyles have begun to rain destruction on Alrest below. Malos is there and waiting. Rex tries to ask whether this is really what Malos wants. He ignores this because he doesn't understand the question, Rex explains that none of his actions were his own will, instead coming from Amalthus's influence. Malos rebukes this and doesn't care what he thinks, using Jin as his main motivation to destroy Alrest. Azurda then explains that if it wasn't for him and Amalthus, Jin and Lora's lives would have been different; Malos agrees, and tells them that he is a "hideous monster, far beyond saving". After the heated exchange, he takes command of Aion and fights the party. At the same time, Shulk and his group can be heard from another universe preparing to strike the final blow to Zanza, prompting the Architect to tell them that his death is imminent. Malos is ultimately defeated by the combined efforts of Rex, Pneuma and Siren. The Conduit begins to fade, and the Architect sends one final command to the Titans before he also vanishes. Malos admits things might've been different if he met Rex earlier, but still insists that only Amalthus could've been his Driver, and dies happy.

With the Conduit's energy gone, the space station begins to collapse, and potentially apocalyse-sized pieces begin to fall. Pneuma forms a plan to reduce the debris, and tells the party where the control room is, so they hustle there. It turns out that she led them to the escape pods instead, and forces them to leave her behind so she can blow up Aion and the whole station, including cashing in the promise that Poppi made in Morytha so she cannot help. Rex is very upset but eventually lets it go. Pneuma sends him the rest of her core; the whole thing drops at his feet and goes dark. The party gets to an escape pod, which Pneuma ejects remotely while she is setting Aion to detonate. The space station explodes, the blast wave destroying the escape pod. Gramps uses a chunk of stored energy that Pneuma gave him to return to his Titan form, saving the party. They descend to find that the Cloud Sea is gone, with the Titans landing in the ocean and joining with newly-revealed land.

Pneuma's Core Crystal regains its colour and glow. There is a brilliant flash, and both Pyra and Mythra appear.