Nephilim

Nephilim Verum is a mysterious girl who often appears as a spiritual being to guide Shion Uzuki throughout the events of the entire Xenosaga trilogy. She acts as an overseer of the flow of time that wants to protect the universe.

Episode I
Nephilim is a mysterious girl who keeps appearing to Shion in visions. Shion first sees her while in the KOS-MOS Simulator, just before Allen pulls her out. When Shion walks close to the Zohar Emulator, she sees her again, walking into it. This causes Shion to nearly touch the Emulator, until Vanderkam yells at her. She also appears, but is unnoticed by Shion when Allen talks to her on the Woglinde. When Shion goes to bed she has a dream of Nephilim, including a mysterious boy approaching her (later revealed to be chaos). When Shion is grabbed by a gnosis on board the Elsa, she has a vision of her again. While on the Elsa, Shion dreams of Nephilim again. Nephilim talks to her about Cherenkov and the fact that it may already be too late for him. Shion has another vision of Nephilim while in the Cathedral Ship, where she tells her to hurry as Cherenkov will soon be gone. When Shion dives into the Encephalon and appears in Old Miltia, she sees Nephilim there at a playground. Nephilim tells her this is the last day Shion spent together with her father. Nephilim reveals her name to her. Nephilim talks to Shion about the world created here in the Encephalon by KOS-MOS and that Shion must return to Old Miltia. After Shion walks off Nephilim talks to chaos, asking him if this is what he really wants and he says yes, that Shion is vital to "her". Nephilim appears at the church where Febronia is located and accompanies the party members as they go into Shion's memories of the Acute Neurosis Treatment Facility. In seeing a vision of KOS-MOS attacking Miltia, Nephilim talks about U-DO, calling it a consciousness that was the source of the space-time anomaly engulfing Miltia. She says she wanted Shion to face her past but she's not ready yet, and there will be a time when she can discuss why if Shion can make it to Miltia. When the Elsa is trying to escape from Proto Merkabah, Nephilim speaks to Shion, telling her to see with her heart, which enables Shion to tell where KOS-MOS is so they can pick her up. Nephilim asks chaos what he will do as the Elsa descends into the atmosphere and starts burning up. There is one final shot of Nephilim as KOS-MOS saves the Elsa from burning up in the atmosphere.

Episode II
Nephilim appears to Shion while she is on board the Dämmerung. She tells Shion that Febronia is waiting for her and that she must go to Old Miltia to make an important choice and save Febronia's sisters. She appears again near the end of the game talking to chaos as the Space Time Anomaly is about to disappear.

Trivia

 * Nephilim has a notable similarity to a young Elhaym Van Houten from Xenogears.
 * In the Japanese versions of both games, Nephilim and Elly share the same voice actor.
 * The pendant worn by Nephilim is similar to the Pendant of Nisan from Xenogears.
 * In Xenosaga 1, when Shion sees Nephilim, said pendant is even seen swinging back and forth similar to the cross animation sequence that appears every time Fei Fong Wong sees himself as a child in Xenogears.
 * Nephilim is named after the sons of fallen angels in the Old Testament.