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After the Federation created the powerful Zohar Modifier, they experimented in linking it to the ultimate weapon, the "Yahweh" Interplanetary Invasion System. This led to disaster, and the project was deemed too powerful and dangerous to continue. It was decommissioned, and both the Zohar and Deus (the central core of the Yahweh system) were stored in its central core. This was the major purpose of the starship. It was then set to leave Federation space to no longer threaten the rest of human civilization.
On the journey, however, Deus became aware of the situation and in self-defense, attempted to take control of the ship. Although the crew attempted to stop Deus from spreading to different sectors, the weapon was found to be too powerful. To prevent Deus from being unleashed upon open space, Shigeyoshi Inoue, the captain of the Eldridge, activated the self-destruct sequence which destroyed the majority of the bridge and engine sections of the ship, which was orbiting above the planet on which Xenogears takes place. The remnants of the starship fell to the planet, along with Deus and the Zohar Modifier. As a result, Deus was heavily damaged and activated its regenerative program, which created a human entity. She set out to begin reproductive processes to create enough biological tissue to repair Deus, birthing Cain, the members of the Gazel Ministry, the first incarnation of Miang and also the first incarnation of Elly before returning to the Kadomony stasis pod from which she was generated. Meanwhile, the Zohar was lost in the mantle of the planet.
There was only one survivor of the Eldridge, and that was Abel or the first Contact, so labeled due to his contact with the Wave Existence, a hyperdimensional being imprisoned within the Zohar Modifier. The Modifier's attempt to answer Abel's desperate longing for his mother during the destruction of the ship resulted in the eventual creation of Elly—it is due to this intervention on the Wave Existence's behalf that Elly, like Abel, retains her memories throughout the generations.
Virtually all the technology seen in Xenogears was a part of the Eldridge, including all the gears with the exception of the Xenogears itself. Examples of Eldridge technology can clearly be seen elsewhere however, most notably Babel Tower and Ft. Jasper. Babel Tower is actually the massive main section of the ship which impacted the planet directly perpendicular to the surface. Ft. Jasper is one of the levitating laser cannons seen active during the opening sequence.
Lastly, the floating island of Mahanon (known as paradise, or god's resting place) which is seen late game is the central core of the Eldridge that still housed the Deus core. After the destruction of the Eldridge, this crashed into the sea.