Plot summary of Xenosaga Episode I

This page describes a plot summary of Xenosaga Episode I - Der Wille zur Macht. It is not a full description nor a complete novelization, but simply an overview of major events. If the reader is looking for a full script, see here.

Prologue

In the year 20XX A.D. at Lake Turkana, Kenya, an archeological excavation is underway, led by doctor Masuda. During the expedition, an altar with a cross-shaped indentation is found at the shore of the lake. When Masuda inserts a silver tablet of the same shape into the indentation, the altar begins to glow, causing an earthquake as underground ruins rise to the surface. After the earthquake subsides, the ruins reveal a golden, cross-shaped monolith which shoots a green-white beam into the sky, leaving Masuda and the rest of the excavation team in awe.

Chapter 1

4000 years later, a team of astronauts are seen securing a similar golden monolith floating in space. When one of the astronauts makes contact with it, they mysteriously disappear. Meanwhile, onboard the Galaxy Federation battleship known as the Woglinde, a team of scientists working for Vector Industries commence a virtual simulation, led by Chief Shion Uzuki. Shion joins KOS-MOS, the Android they're testing, inside the simulation where they traverse the ruins of a 21st century city-scape. After the appearance of a mysterious girl, the simulation begins to malfunction , prompting Shion's fellow employee Allen to pull her out of the simulation. Shion then leaves to take the combat data to the ship's captain, Kazuichi Moriyama. On her way, she comes across Lieutenant Commander Vanderkam berating his subordinates and reminisces of her previous superior, Kevin Winnicot. When Shion spots the golden monolith that was just retrieved, she approaches it and finds herself in a mysterious graveyard with the same mysterious girl from the simulation. However, she's interrupted when Vanderkam tells her off for getting too close to the monolith.

Allen catches up to Shion to hand her the combat data disk that she left behind at the lab. Shion gets a call from Caspase to help with Realian maintenance. There, she performs counseling to the various combat models before Luis Virgil shows up. Virgil shares his extremely unfavorable opinions towards the rights of Realians, challenging Shion's progressive stance before he leaves the lab feeling ill. Shion leaves to deliver the combat data to the captain, but Commander Andrew Cherenkov scolds her for only turning over simulated data, expressing worry that the Gnosis will attack any second before receiving an abrupt message. In private, Cherenkov's superior Margulis berates him for the carelessness of handling the "Zohar Emulator" and orders him to keep it safe until reinforcements arrive, as well as to encourage the KOS-MOS development team to hurry with its deployment. Back at Shion's quarters, she gets into an argument in a call with her older brother Jin before going to sleep. She dreams that she's in the graveyard that she saw when she approached the monolith and notices the phantom girl before she is greeted by the silhouette of a boy.

Chapter 2

On the bridge, an alarm goes off as the Woglinde is about to gate jump, pinpointing the source as the Vector lab. At the lab, KOS-MOS is starting up on her own despite having that ability disabled two years prior. Shion wakes up and realizes what's going on, remembering the incident that killed Kevin. On the bridge, the crew realizes that the Gnosis are about to gate out. Not long after, the Gnosis begin to attack the ship and its crew, tearing Realians to shreds and turning humans into salt. As Shion avoids Gnosis making her way to the Vector lab, she is nearly shot down by a barrage from Virgil's A.G.W.S. squad. One of the combat Realians directs Shion to an escape pod before he joins the rest of the combatants to hold off the Gnosis ambush despite Shion's protests. Meanwhile, Cherenkov, Vanderkam, and various other rogue soldiers are making plans to ensure the Zohar Emulator gets to Margulis. Cherenkov voluntarily decides to sacrifice himself while the others escape as he purges the block. On the bridge, the captain deduces that the Gnosis are after the object in the hangar. The crewmembers attempt to call for reinforcements, only for a Gnosis to collide with the bridge, killing everyone within.

Virgil's futility in stopping the Gnosis' advances leads him to steal Shion's control terminal to use the combat Realians as bombs. Horrified, Shion tells him to stop, only for him to invoke the Miltian Charter, solidifying his jurisdiction over the situation. Shion demands him to stop, but he detonates them regardless. Unsurprisingly, the Gnosis survive the blast and one grabs Shion. As her body turns white, Shion sees a vision of the mysterious girl. Suddenly, her body returns to normal as a beam frees her from the Gnosis' grasp. KOS-MOS bursts through the wall alongside Allen. As Shion recovers from the attack, KOS-MOS activates the Hilbert Effect and makes short work of the remaining Gnosis in the area. KOS-MOS orders the survivors to proceed to Hangar 1 and she concludes that the Gnosis' target is the Zohar Emulator.

Shion notices that all but one escape pod has been used before noticing Cherenkov, who was unable to purge the block. Shion then grabs a rifle and joins the survivors in fending off the Gnosis. As Allen, Virgil, and KOS-MOS are fighting the Gnosis, KOS-MOS suddenly fires rounds through Virgil, killing him. As he dies, he sees a vision of a silver haired woman. Shion scolds KOS-MOS for killing Virgil, only for her to specify that she was programmed to protect Vector personnel, not members of the military. KOS-MOS remains unfazed by Shion's continued objections, insisting that killing Virgil was the best possible outcome. Despite everyone's efforts, the Gnosis still manage to escape with the Zohar Emulator and destroy the Woglinde, with only Shion, Allen, KOS-MOS, and Cherenkov onboard the last escape pod. KOS-MOS then receives mysterious orders to head to Second Miltia.

Chapter 3

A passenger ship called the Elsa, comprised of Captain Matthews and his mates, Tony and Hammer, traverses the wreckage of the Woglinde in hopes of salvaging the remains to pay back Matthews' debt to their boss. As they begin their salvaging efforts, KOS-MOS collides with the window and the crew mistakes her for a dead body. To their shock, she demands that the crew lets her into the ship, going as far as threatening to kill the crewmembers if they don't. Soon after they comply to KOS-MOS' demands, Shion manages to make contact with the Elsa and orders KOS-MOS to let her onboard. KOS-MOS refuses as she estimates that a Federation rescue crew will arrive soon. However, Shion threatens to open the pod's hatch with her and Allen inside if KOS-MOS does not comply to her demands. Another crewmate named chaos, was woken up by the commotion and encourages KOS-MOS to let them onboard, to which she finally relents. On the bridge, as the survivors introduce themselves and apologize for KOS-MOS's rashness, a stray Gnosis manages to sneak on board and attack Cherenkov. chaos uses his power to make the Gnosis disappear and save Cherenkov.

Meanwhile, Vector Industries' CEO, Wilhelm, receives a report on Shion's rendezvous with KOS-MOS from a red cloaked man. He reveals there is an unidentified ship closing in on the battlefield. Wilhelm inquires that, if the ship were to threaten Shion, KOS-MOS would protect her. The cloaked man verifies this. Wilhelm claims pulling back KOS-MOS was the right choice as he believes there is no need to continue serving the Federation. Wilhelm also mentions that the data for something called the "Rhine Maiden" is now complete, and that everything is moving as specified by the "Compass of Order". He orders the cloaked man to gather the necessary factors and wait for "the other one" to awaken.

At his hideout, Margulis and his second in command, Pellegri, review footage of the planet Ariadne's disappearance. Margulis expresses little remorse for the loss of half a billion lives, but Pellegri insists that the innocent lives deserve respect. Margulis goes further to express the means he would take to get results, even going as far as saying he'd use the Original Zohar. He presses Pellegri over her indecisiveness before one of the nearby soldiers informs him of a message from Vanderkam, reporting that all of his forces were wiped out and that they lost the Zohar Emulator due to it being taken by the Gnosis. Disappointed, Margulis tells the soldier to prepare the 474th Spec Ops Fleet for the implementation of "Plan 31".

At the Federation Capital Fifth Jerusalem's Orbit Tower, members of the Subcommittee on Close Encounters discuss a certain cyborg and his history of choosing particularly difficult missions before they summon him into the meeting room. They send the cyborg, named Ziggurat 8, on a mission to infiltrate the asteroid base Pleroma, a hideout for the U-TIC Organization, to retrieve the prototype for the 100-Series Realians, a young girl with pink hair. After Ziggurat 8 departs, one of the subcommittee members, named Juli Mizrahi, reveals that Ziggurat 8 ended his past life by shooting himself in the head, causing the other members to question if they can trust him to complete his mission.

As Margulis interrogates the girl on the Pleroma, Ziggurat 8 infiltrates the base using a cloaking device by smuggling himself on one of U-TIC's dropships. In a flashback, Ziggurat 8 is further briefed on the mission by Mizrahi, saying that the data the girl holds could affect the fate of humanity, and that the U-TIC Organization wants to get their hands on that data for themselves. After Ziggurat 8 knocks out the guards and frees the girl, an alarm prompts the two to escape, but only after the girl identifies herself as MOMO. The two hide in the security station and Ziggurat 8 introduces himself and explains his backstory as an organ donor who was resurrected after death due to the Life Recycling Act. MOMO dislikes the name and nicknames him "Ziggy". This triggers a flashback from Ziggy's former life, where he gave his son a robot dog as a gift. MOMO wonders if her choice of nickname sounds too much like a dog's name, but Ziggy accepts it. Just moments away from freedom, Margulis ambushes the duo and defeats them with ease. However, Ziggy detonates a device he planted earlier and hijacks a U-TIC gunship to make their escape. As U-TIC soldiers begin to chase after them, a white haired man and a silver-haired Realian step out from the shadows.

Chapter 4

Meanwhile on the Elsa, the crew bonds over dinner. While washing the dishes, Allen admits that he checked the ship's registry, identifying its crew as affiliates of the Kukai Foundation, quoting rumors about the Foundation "crawling with mutants". Shion rebukes him for this "racist comment", defending the Foundation and lecturing him on its history. She further clarifies that it hasn't officially been demilitarized yet and that its current director protects victims of the Life Recycling Act. chaos then comes in to help wash the dishes before noticing a spare plate of curry for Commander Cherenkov. chaos then visits the sleeping KOS-MOS below deck and questions where her "real self" exists.

After chaos leaves, Cherenkov walks up to KOS-MOS and has a flashback to two years prior when he and his U-TIC subordinates broke into a Vector lab on Carioca with the help of a cloaked man. In the lab, a prototype KOS-MOS called the "Archetype" malfunctioned and began to kill U-TIC soldiers and Vector employees indiscriminately. When the flashback ends, Shion suddenly walks in on Cherenkov to deliver the curry. The two discuss Virgil's death at the hand of KOS-MOS back on the Woglinde. At the S.O.C.E. building, the subcommittee members discuss the success of Ziggy's and the matter of Joachim Mizrahi's Y-Data, hidden inside MOMO. In the event that MOMO is unable to be brought to safety, Juli brings up the subcommittee's other lead, a young boy from 14 years ago who seemed to be Mizrahi's assitant. The resulting discussion reiterates that their goal is to gain access to Old Miltia and retrieve the Original Zohar.

On a call with her director, Shion demands that she not turn over KOS-MOS to Second Division yet because KOS-MOS is acting on her own accord. After much back-and-forth, the director relents. At the same time, Ziggy and MOMO are traveling in the same hyperspace column as the Elsa to escape their pursuers. The Elsa gets caught in the battle and retaliates against the attackers, saving Ziggy and MOMO's ship in the process. After the attack, the crew has dinner and gets to know MOMO and Ziggy.

Meanwhile, Margulis receives reports from a U-TIC spy within the S.O.C.E. and Cherenkov. A white-haired man, Albedo Piazzolla and his Kirschwasser enters the frame and head out on the E.S. Simeon to pursue MOMO. Meanwhile, while piloting an A.G.W.S. in space, a red-haired boy called Jr. is investigating the disappearance of Ariadne with the crew of his ship, the Durandal. Jr. is joined by his colleague, Mary Godwin as they come across the wrecked remains of the Woglinde. The U-TIC Mothership arrives and destroys what's left of the Woglinde. Fortunately, Jr. and Mary make it out just in time. As Jr. returns to the Durandal's bridge, the crew assumes battle formation against the U-TIC fleet and wins by ramming the Durandal into the mothership. Accompanied by Mary and an unnamed soldier, Jr. breaks in and has Mary begin downloading data from the ship's mainframe, but are interrupted when U-TIC soldiers ambush them. Jr.'s reckless gunmanship unintentionally cuts off the mainframe before Mary can finish their work.

Meanwhile, the Elsa decides to stop for repairs at the Dock Colony. Cherenkov leaves the ship on his own and gets cornered by a group of hoodlums who beat him up out of hatred for the military. In retaliation, Cherenkov nearly kills the hoodlums, leading Shion and the others to find them bloodied and in critical condition on the floor. Back on the Elsa, Cherenkov lies about what happened to make it seem like the hoodlums fought each other. That night, Cherenkov notices that his hand is beginning to fade away. Shion has a dream where the phantom girl tells her that she may be able to understand "him" in his final moments, even if it's too late. Back on the Durandal, a warning alert goes off in the Isolation Area. Shelley concludes that it's resonating with something out in space, prompting Jr. to commence a gate-jump.

The Elsa is then forcibly dragged out of hyperspace by a swarm of Gnosis, led by a planet-sized Gnosis known as the Cathedral Ship. The party is swallowed by the Cathedral Ship, realizing that they have been separated from the Elsa and its crew, and begins looking for them. While exploring, the party notices a human-made object assimilated into its interior, deducing that the Cathedral Ship was once a planet. Shion then experiences another vision of the phantom girl, warning her that "he" will be gone soon. Separated from the rest, Cherenkov hallucinates that he's in a crowded city before opening a door into a war-torn field of bodies. Cherenkov has flashbacks to his previous life, having undergone Personality Reconditioning as a sentence for a string of murders he committed. At one point he was married to his attorney, but ended up killing not only her, but also her clone. Before he could receive the procedure for Level 9 Personality Reconditioning, he killed the staff of the facility he was detained in. Shortly after, he was discovered by Margulis and recruited for the U-TIC Organization.

The party arrives at the center of the Cathedral Ship, which consists of what appears to be a building surrounded by a large Zohar-like monument. chaos theorizes that this area is important to the Gnosis before KOS-MOS loses the Elsa's signal. As Cherenkov's condition worsens, he reminisces about the day of Ariadne's disappearance. Under Margulis' orders, he was to commence a Link Experiment with a Zohar Emulator. This resulted in a localized Space-Time Anomaly, forcing Cherenkov and the U-TIC forces to evacuate from the planet. As they ascended into orbit, he hallucinated his wife and cloned daughter. Back in reality, Cherenkov starts to see visions of ghosts.

When the party reaches the center, they find the Zohar Emulator that was taken from the Woglinde. Cherenkov appears and admits his role in the disappearance of Ariadne as he fades in and out of visibility. Cherenkov then freaks out over unseen entities before being struck by a spirit. As more spirits enter Cherenkov's body, the Emulator glows and he transforms into a bestial Gnosis. The party defeats the monstrosity and Shion experiences flashbacks of Cherenkov's life before she finds herself on an empty beach with Cherenkov. He says he thought the world rejected him, but that he was the one who really rejected the world and that this beach makes him feels at peace. Back in reality, Shion breaks down and chaos comforts her. The Elsa and the crew arrive to rescue the party.

Chapter 5

As the Elsa escapes the Cathedral Ship, they are pursued by the remaining Gnosis. The Durandal appears, but not even its assistance is able to stop the onslaught. When all seems to be over, KOS-MOS decides to go outside the Elsa. Shion demands her to come back as she is not equipped to destroy that many Gnosis, only for KOS-MOS's eyes turn blue before uttering "Shion... Will feeling pain... make me... complete?". Meanwhile on the Durandal, a 100-Series Realian informs the crew that the Zohar Emulator's waves can no longer be suppressed, before Shelley alerts the crew that there's an intruder alert in the Isolation Area. Jr. orders to cut off the main line to the Isolation Area. On top of the Elsa, KOS-MOS' abdomen opens up as she watches the approaching Gnosis, revealing a cannon and a materialized crystal-like propulsion on her back. She then blasts all of the Gnosis, absorbing their remains into her torso. Her eyes then turn back to red.

Stunned, Shion tries to gather what just happened before Jr. hails the Elsa crew. As Matthews talks to Jr., Shion wonders if Kevin might have had something to do with KOS-MOS' newly revealed power. The Durandal retrieves the remaining Zohar Emulator floating in space. On the Durandal's bridge, the party meets the Elsa's boss, Gaignun Kukai Jr. otherwise known as Jr. He then plots a course to the Kukai Foundation to repair the Elsa. Jr. orders Shelley to change course to the Foundation and tell Gaignun that they have secured the final Emulator. As the Durandal gate jumps, the E.S. Simeon is seen spectating from behind.

Chapter 6

Jr. has a nightmare of him on Old Miltia, running from an unseen force. He sees a dead cat named Gaignun and finds himself carrying an unconscious young boy before a lights envelops them. He then falls into a red abyss before waking up in reality. The next day, Jr. shows the party the Kukai Foundation's Isolation Area for the Zohar Emulators. MOMO and Shion express curiousity about the room across from them. Inside, the party sees several Gnosified corpses with the one in the center looking notably humanoid. Jr. explains that humans who are touched by a Gnosis usually turn white and shatter into pieces, but there are exceptions such as the one in the center he calls Betty. Shion remembers having survived almost turning into salt and asks Jr. if there are any exceptions. Jr. denies any known exceptions, worrying Shion. Jr. explains that it wasn't until the Miltian Conflict that Gnosis were brought to the forefront of history thanks to Joachim Mizrahi. As Jr. explains the purpose of the Kukai Foundation, MOMO is notably upset about her father's alleged reputation and leaves the room. Shion later finds her at the Durandal's park while she ponders the reason for her birth. Shion empathizes with her, noting all of the good inventions Joachim Mizrahi brought to the world. Allen then barges in, telling them that, after docking at the Kukai Foundation, they will be dropped off at Second Miltia. Shion thinks it a little odd that everyone on the ship is heading to Second Miltia.

The Durandal then docks at the Kukai Foundation, turning the ship into a skyscraper, leaving everyone in awe. The director, Gaignun Kukai, accompanied by his aids Mary and Shelley, greets the party. As Shion shakes his hand, she notices a red "669" imprinted on his palm. He then focuses his attention to MOMO, telling her that he'll get her to Second Miltia safely and that Juli Mizrahi told him to take care of her. MOMO wants to meet her but Gaignun tells her that she's very busy. In Gaignun's quarters, Gaignun and Jr. talk about KOS-MOS before wondering if Shion may be on to their secrets. They also speak of the "Zohar Project" before Gaignun gifts Jr. with a stainless-steel Makarov, reminding him to act his age, seeing as he's "older" than Gaignun.

Allen visits Shion's quarters and notices that Shion has been acting gloomy lately, but Shion denies it before Allen reminds her she can confide in him. Jr. then barges in, asking Shion to come and play. At the beach, as the rest of the party play, Shion contemplates KOS-MOS's ability to express empathy. Allen and MOMO then interrupt her in the hopes of including her in the fun, and MOMO wonders how difficult it is to work on KOS-MOS. Allen adds that she has a ton of black boxes, saying that they're trying to take it apart piece by piece so that they can recreate KOS-MOS's original form. Shion then changes the subject, sparking up a conversation about rumors regarding Jr. and Gaignun's familial ties. Jr. overhears their conversation and boasts about the beach's weather-changing features, starting a thunder storm that inadvertently triggers Shion's astraphobia. In his office, Gaignun provides a report to Representative Helmer on MOMO and the retrieval of the final Zohar Emulator. He then brings up his concerns about the U-TIC Organization's activities, worried that they may attempt to awaken U-DO.

Meanwhile, in a conversation between Sellers and Margulis, the latter doubts the possibility of them being able to find or open the door to Lost Jerusalem. Margulis reveals he's proceeding with Plan 401. Sellers objects, reminding him that MOMO is in Gaignun's custody, to which Margulis proposes "him" as a countermeasure. Margulis then gets in contact with Albedo, ordering him to be on standby, not to interfere with Plan 401 and if the plot fails, he is authorized to use the Song of Nephilim. Pellegri express her disgust of Albedo, a U.R.T.V. who was born from Life Recycling, worried that he might become impatient and act on his own, only for Margulis to talk her down, saying that's not in his nature and claiming that MOMO is the only thing that interests him.

As Shion and Allen do maintenance on KOS-MOS, the Durandal is about to enter the Miltian star system. Meanwhile, Jr. approaches MOMO and gives her a lucky charm, a bullet on a chain that says "sayonara baby". Suddenly, a group of Federation ships surround the Durandal and open fire, knocking out power for a couple of seconds. At the Federation Parliament Building, the senators review footage depicting the Durandal attacking the Woglinde, justifying their rights to strip the Second Miltian Government and the Kukai Foundation of their rights before getting into contact with Juli, asking her opinion. She says that MOMO was to be moved to Second Miltia per her plan. The senators refute this and continue arguing with each other, prompting the chairman to demand order. He then contacts Helmer to ask his input on the situation.

In a communication, a Federation soldier tells the Kukai Foundation that they are under arrest , warning that if the Durandal docks with the Kukai Foundation, they are authorized to use lethal force. The party is confused by this development before they see doctored footage of the Durandal destroying the Woglinde on the news. chaos is impressed by how they perfectly synchronized the battle coordinates and Jr. realizes that it was from their prior fight with the U-TIC Organization. Shelley suspects that they must have infiltrated the Federation government and military. Shion proposes testifying as a survivor of the Woglinde disaster, but Gaignun claims that they'd only have suspicion cast upon them as part of the conspiracy. As the Federation fleet surrounds the Kukai Foundation, the arresting officer, Lapis Roman introduces herself and orders the arrest of the entire Durandal crew, taking the party as witnesses. She then orders to confine them into a single room and keep an eye on them.

While confined, the party discusses what could have brought these events to pass, considering that MOMO may be their goal and that U-TIC members could have been planted within the Contact Subcommittee. In the halls of the Durandal, Lapis puts Gaignun in contact with Representative Helmer, who reveals Lapis is his agent sent to infiltrate the Federation to keep tabs of the U-TIC members within it. He asks Gaignun to assist her in her investigation. Helmer then hangs up and takes another call from Wilhelm. They talk about the current dilemma and U-DO's awakening before Wilhelm offers aid in clearing Second Miltia's name. Back on the Durandal, Lapis reveals to the party that she and another federation officer are Second Miltian agents. As they discuss methods of clearing their names, Shion proposes using KOS-MOS's battle data from during the Gnosis attack. To make things convincing, the party knocks Lapis and the other soldier out so they can reach KOS-MOS's maintenance room and begin an Encephalon dive.

Inside, Shion, chaos, and Allen find themselves outside a large tower, seeing a child version of Shion on the swings before her father calls her to come home. The phantom girl appears, introducing herself as Nephilim. Jr., MOMO, and Ziggy find themselves in a barren city observing child soldiers, identified by Jr. as U.R.T.V.s. Jr. confirms that they're in a memory of the Miltian Conflict from 14 years prior. As the three make their way among the chaos of the city, the U.R.T.V.s are seen killing indiscriminately. A young Gaignun kills some of the out of control U.R.T.V.s looking for "Rubedo". Jr. sees a vision of a young, wounded Gaignun being attacked attacked by a young Albedo, surrounded by a red aura.

Nephilim confirms to Shion that this place is indeed a memory of Miltia created by KOS-MOS. Shion wonders how that's possible, knowing that she destroyed the original KOS-MOS two years ago, when Kevin was killed. Nephilim tells Shion that she must confront her past here; the day her parents were killed during the Miltian Conflict. Jr., Ziggy, and MOMO find themselves in front of the large tower, Labyrinthos, with the sky lit up. MOMO watches as her father, Joachim Mizrahi falls to his death from an explosion. MOMO runs to catch him, only for him to vanish on impact. The scenery then disappears, causing the three to fall into nothingness before being engulfed by light.

In a forest, Shion, chaos, and Allen reunite with Jr., MOMO, and Ziggy, and head towards a church in the distance. Inside, they find a silver-haired Realian woman named Febronia, who takes care of the church. Shion briefly remembers Febronia being eaten by a group of inhuman-looking Realians before snapping back to reality. She claims she remembers Febronia, but doesn't want to remember. Nephilim then appears, telling Shion that stepping through the back-door of the church will allow her to confront her worst memories. When she opens the door, the party finds themselves in the Acute Neurosis Treatment Facility, where Shion's mother was hospitalized. They enter the room and Shion sees the corpses of her parents as several inhuman-looking Realians fuse together. Meanwhile, Jr. sees Albedo monologuing and laughing maniacally. The traumatic visons fuse into one being, representing Shion and Jr.'s traumatic memories. Although the two manage to defeat it, they remain psychologically unstable and are brought to a grassy plain where Febronia sits with two young, Realian girls running around her; Cecily and Cathe. The scenery then changes to a grim, desolate version of the previous area. Febronia explains that the two girls are trapped in a creation of mankind to control the Zohar. She asks Shion to set them free for the future of all life.

Nephilim then shows the party a vision of the future, where KOS-MOS confronts a stream of energy and consciousness known as U-DO near Miltia. Nephilim hopes to show them this in the hopes that it would be preventable. However, she acknowledges that Shion and Jr. are not yet ready to confront their pasts and presents them with a door. Shion opens the door to find KOS-MOS tied to a stone monument. Shion retrieves the data from her and the party exits the dive. KOS-MOS wakes up and Shion presents KOS-MOS's data to Lapis. However, she advises them to remain in the Miltian star system until the charges are dropped. chaos and Allen later have a conversation at the Durandal's park, where Allen confides in chaos his worries about Shion.

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Chapter 7

Meanwhile, in a dimly lit room, with Albedo carrying a dead Kirschwasser. Margulis informs him that they evaded the trap they set, and gives him the order to use the Song of Nephilim, prompting him to laugh with glee and drop the Kirschwasser's body on the floor. On board the Elsa, chaos at workstation is starting to feel uneasy, Jr. and Gaignun in his quarters take notice of the Song of Nephilim to their shock. chaos suddenly jumps from his workstation, warning that "they must not play the Song", confusing his crewmates. At Wilhelm's office, as the room shakes, Wilhelm and the Red Testament are seen playing chess and they too take notice of the Song.

Suddenly the Gnosis gate out in front of the Kukai Foundation. Shelley gives the evacuation order and KOS-MOS activates the Hilbert to buy time for the evacuation. Down on the surface, the party evacuates as many citizens as they can. In space, Simeon is seen destroying everything, whether Federation ships or Gnosis, madly gloating in the process. During the evacuation, MOMO volunteers to stay behind to aid the injured. However, when Shion returned to the Kukai Foundation, MOMO is nowhere to be seen. Shion asks the party if they seen MOMO and they say no. Meanwhile, MOMO finds herself at a facility, remembering following a man that resembles her father before it turns out to be Albedo. As she explores her surroundings, she comes across a motionless Kirschwasser, who briefly wakes up a transfers a memory of MOMO before becoming motionless again. This memory depicts MOMO's birth in a test tube before the scene changes to Albedo killing the Kirschwasser and laughing madly.

Back at the Kukai Foundation, the situation worsens, forcing the commander of a Federation ship to decide to target the Kukai Foundation to hopefully destroy the source of the Gnosis phenomenon. Shelley takes note of the Gnosis, movement, with Jr. telepathically communicating with Gaignun confirming that the source of the Gnosis is the Song of Nephilim. Shion surprising hears it as well, surprising the U.R.T.V. survivors. Meanwhile, MOMO comes across a dimly lit room with Albedo carrying a dead Kirschwasser who then breaks her arm before tossing it aside. He then pulls out a knife and threatens to slit MOMO's throat with it. He continues menacing her by cutting off his arm and head with it, allowing his severed head to taunt MOMO. When Albedo learns that Jr., Rubedo is alive, he grew more maniacal than ever, MOMO then passes out as Albedo madly laughs.

As the Gnosis continue to gate out, the just as the commander gives the order to destroy the Kukai Foundation, he was interrupted by colossal blast, the Rhine Maiden that destroys a lot of Gnosis. The blast comes from the Dämmerung gating out with three other ships, much to Shion's surpise. All four ships fire the Rhine Maiden again to destroy more Gnosis. Miyuki gets in contact with Shion and transfer a PT Cartridge for KOS-MOS to use. She theorizes by linking the Dämmerung's mainframe with KOS-MOS's D.S.S.S., they may able to reveal what's attracting the Gnosis. In space, KOS-MOS loads the PT Cartridge into her handcannon which transforms into a large cannon, which fires at the source of the distortion, revealing the Song of Nephilim. At the same time, Albedo notices that they're found them before deciding to intrude into MOMO's memory.

Chapter 8

Jr. and the 100-series Realians conclude that MOMO is on board the Song of Nephilim. Ziggy opts to go it alone, but is stopped by Jr. and the rest of the party, citing their own reasons to rescue MOMO which he relents. The party boards the Elsa and enters the Song of Nephilim. During the ride, Shion remembers the pattern on top of the Song of Nephilim is the same one from his mother's hospital room. Inside, the party finds an unresponsive MOMO and angered that Albedo has taken her consciousness. Eventually, the party reaches the central chamber with him still intruding on MOMO's memories. It turns out that the MOMO that joined them is a Kirschwasser in disguise who the proceeds to choke Jr. only for him to unleash a blast that disables her. Jr. attempts to kill him, but all efforts were proved useless has he regenerated his destroyed body parts. As Albedo dives into MOMO's memories, he is blocked by an image of KOS-MOS and a naked Shion and was pushed back. He then decides to fight the party with E.S. Simeon but is defeated. On foot, Albedo eggs, Jr. to use his full powers and which he does, only for MOMO to stop them, only for Albedo to cruelly mocked the dead Kirschwassers across the room, infuriating Shion. Suddenly, a blue-colored Testament appears and orders Albedo to leave. Jr. tries to go after him but is blocked by the new enemy who then transforms to battle the party, but is defeated as well.

Chapter 9

With nothing left to do, the party returns to the Durandal and decides to destroy the Song of Nephilim. However, the laser blasts reflects off and reveals a new facility: Proto Merkabah, commandeered by none other than Albedo. He uses it to absorb the remaining Gnosis and destroy the entire Federation Fleet with it before targeting Second Miltia with it.

Chapter 10

The party then ventures inside Proto Merkabah to destroy the core but is blocked by Albedo. He then battles the party personally but is defeated, but not before he unleashed a giant Gnosis fused with the reactor as a distraction as he makes his getaway. The party manages to destroy the Gnosis and shut down the reactor.

Chapter 11

However, Proto Merkabah is set on a collison course with Second Miltia, threatening to destroy the planet if not stopped. KOS-MOS decides to stay behind and detach all the sup-compartments to break it up so the pieces burn up in the atmosphere harmlessly. As the party returns to the Elsa, Jr. becomes nervous as the facility begins to fall apart. Matthews eggs him to take ovff, and he does so reluctantly. Shion protests that they're leaving KOS-MOS behind, but a message from Nephilim tells her to see with her heart, directing Tony to the wall where KOS-MOS barely manages to return to the Elsa in one piece. However, as the Elsa escapes from the collapsing Proto Merkabah, the approach angle of reentering Second Miltia is too steep and threatens to burn up the ship as well.

Chapter 12

In the hanger, chaos notices KOS-MOS acting strangely, uttering "Relinquish your pain... unto me...". Back on the bridge, Hammer notices the aft hatch is opened, Shion realizes it was KOS-MOS and she is going to create an energy shield to protect the Elsa and orders her to stabilize the ship at that time. Shion protests, she won't allow her to destroy herself to save the crew, but she hangs up. Back in the engine room, as chaos hands glows, a scene cuts to Nephilim at a graveyard, a boy playing with blocks, and Wilhelm observing the Compass of Order going haywire. KOS-MOS then produces a wing-shaped shield that shields the Elsa, but destroys her Hilbert Emission helmet in the process.

When the party comes, they find themselves in one piece with KOS-MOS, without her helmet, standing on the Elsa as it descends to Second Miltia. The scene later cuts to Jin kneeling to a grave of his parents as pieces of Proto Merkabah reenters the atmosphere with the Elsa flying over. In another scene, Gaignun is in a phone call with his superior, talking about the U-TIC Organization and Albedo. The scene changes to Albedo and E.S. Simeon declaring that his mission is complete, warning Jr. before laughing manically. The next scene depicts the Red Testament and Wilhelm, learning about Albedo's ascension, saying that he can open the way to Abel's Ark. Back on the Elsa, KOS-MOS returns to the bridge with Shion greeting her with "Welcome Back."