So, the machine that Fei aquires is actually an ancient mecha that connects to the Zohar, which Fei is also connected to because he was on the spaceship that was transporting it and the Deus superweapon thousands of years ago, but because of his connection with the Zohar, Fei has been able to reincarnate and basically be responsible for all the major events that have happened in the history of the world, also the world has effectively ended several times, but more on that later, no, Fei and his girlfriend have reincarnated several times and have always managed to find eachother and screw up something in the world together, and the reason that anybody even exists on the world that they are on is because the Deus made them so that they would spread out and breed, just so that it could change people into monsters and use them to repair itself, and also it made a woman who would attempt to see that through, but that woman lives in all women, and if she dies then she makes some other woman's hair purple and takes over her body instantly. Also, the Zohar is actually a higher-dimensional being that wants to be returned to it's own dimension, but it also powers all the super robots of the world and lets people use magic. The super robots are all supposed to be ancient war machines, but the people of Sol apparently manufacture their own somehow, as they apparently send several new machines at you. Fei, the main character, is also two of the games antaganists, one of them is is alter ego that was created because he couldn't handle the torture/testing that his then purplehaired mother put him through, the other is a past version of himself that somehow exists even with him being reincarnated, both have their own robots, even though his alter ego's machine is actually just Fei's own machine, just transformed. Deus is worshipped as a god and your robot is actually supposed to be the instrument that destroys it. This isn't even touching on the girl with the giant robot that carries the soul of her father, the stuffed animal that grows as large as your giant robots and it actually some kind of weird pink creature, the small girl that is actually a being composed of nanomachines and was created in a past life by Fei, Fei's dad being possessed by Fei's past self, the various religious examples and references.
Basically the whole story is a crazy, mixed up, anime-filtered version of the Bible...with robots.