- Yabeh/Deus was the superweapon being carried aboard the Eldridge at the start of the game; proving uncontrollable, its creators attempted to destroy it. This failed, however, as its remnants simply fell to this planet. It created Cain, Miang and the Gazel Ministry to ensure that humanity would repopulate the earth and provide the means for its rebirth. Zohar is its power source and Merkava is its "ark", while Kadomony is the "Persona" and means by which it generates organic material.
- As a result of this, Miang has existed since the beginning of this planet's history, transferring her mind to another woman each time she died. One such victim was Fei's mother, Karen Wong, who performed the inhumane experiments that led to the birth of Id.
- The Coward and Id both blamed one another for Karen's death and failed to see the truth of the matter, leading to Id's rampage and Khan intervening to create the third personality (the one we've followed for much of the game) to keep Id in check.
- Grahf and Lacan are indeed one and the same person. Grahf was created when Lacan, anguished after Sophia's death, came in contact with the Zohar; his anger and emptiness gave rise to a violent, nihilistic personality obsessed with power and the world's destruction.
- Fei is continually reborn throughout history in different guises as a result of his role as the "Contact", an entity granted power by the Zohar and the "Wave Existence" therein which seeks freedom from its prison. Four such incarnations are shown in the game - Abel (the original), Kim (the Zeboim scientist who gave rise to nanotechnology), Lacan (the painter who would become Grahf) and Fei Fong Wong.
- Elly is Fei's "antitype" who separated from Miang. She too is fated to continually be reborn alongside him, always dying a violent death. She embodies the Wave Existence's will and Fei embodies its power.
- Krelian's obsession with Elly stems from his former love of Sophia and his anger at her death, leading to his desire to "create god".
Various factoids and symbolism
- The Ark is a reference to the story of "Noah's Ark", where Noah was ordered by God to build an ark and save two of every animal from a great flood.
- Seraphim are said to be the highest order of angels and direct servants of God, who surround His divine throne.
- Rene and Roni's names are probably familiar to anyone who played Final Fantasy 6; they share their names with the characters Sabin Rene Figaro and Edgar Roni Figaro. This is not a coincidence, as their characterizations and story scenes were also written by Kaori Tanaka (aka Soraya Saga), one of the three head writers on Xenogears.
- "Har" literally means "tell", a type of archaeological mound created by human occupation and abandonment. It's commonly associated with the phrase "Armageddon", in which a climactic military amassment at the Har of Megiddo is said to bring about the end of the world.