Xenogears

Full Story, spoils everything:

"In the beginning, Deus was created. This has made a lot of people very angry and has been widely regarded as a bad move.

The creation of an unknown spacefaring civilization, Deus was originally intended to serve as a biological weapon. To power Deus, an entity known as the Wave Existance is summoned from another dimension and trapped inside Deus's engine, Zohar. However, its creators deem Deus too powerful to use, and they attempt to dispose of it by shipping it...