<div style='font: 12pt ; text-align: left; '>You probably know all this already, but I just played Xenogears a few months ago so a lot of this is still fresh in my head:
It's a fairly important part of Xenogears since it is what gives all the Gears on the planet their energy source (though Gears still need fuel for whatever reason). Plus it is also linked to all the Ether abilities. The way the Deus weapon was supposed to work is that there were 4 things, the Raziel Tree (the super computer), the Zohar modifier (unlimited energy source. Abel, Grahf, and Fei all made contact with it, Grahf's contact was incomplete though), the life generation computer (forget its name now), and then Deus which is actually a modified or genetically engineered creature related to the Genosis.
As for Perfect Works, it outlines a lot of things seen in Xenosaga.
Sometime in the early part of this Millenium the Zohar modifier was discovered in Africa. It supposedly was the origin of existance, inside it was trapped a piece of "God" (The Wave existance); actually I don't remember exactly, but I think it might have been when they built the Zohar power generator that they trapped the wave existance (which Krelian merged with at the end of Xenogears). They also developed a way to harness this energy. There was also discovered "Magnetic Anti Matter" or something like that (MAM), and by 2500 the study of the Deus weapon began.
They used the Zohar modifier to perfect their space travel and somehow Earth became uninhabitable and untouchable by Humans. They named the planet "Lost Jerusalem". Their new capital at the middle of their empire they called "New Jerusalem".
They constructed the Colony ship Eldrige and finished the Deus weapon. I can only guess as the story goes that the events at the beginning of Xenogears took place close to Earth, but I can't be sure since I am only guessing. The world of Xenogears was the third planet, like Earth is. Anyways, as it goes, the Deus weapon took over the Zohar power source and the ship. The captain set the Eldrge to self destruct, and everyone went to escape, everyone was destroyed and only Abel survived. Abel had made contact with the life computer (forget its name) and it had terriformed the planet (maybe Earth) and created True Miang to act as "Mother Earth", but True Miang split into Elly and Miang (or something like that).
Anyways, Perfect Works also goes over the Genosis, KOS-MOS, and the dissapearing planet and such. Xenosaga isn't the same because they have updated the story, but generally it's the same outcome.
Xenogears doesn't surround the Zohar Modifier, but it is a very important part of the story since it is what is behind all the intentions of the villains, especially Grahf and Krelian. At the end, the Wave Existance is freed and Krelians Soul Joins it in returning to the fourth dimension (or something like that). Abel, Grahf, and Fei are the same person (just reborn into different bodies), and all of them made contact with the Zohar Modifier (which powers everyones Ether abilities, and the Gears).</div>
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