Completely random theory about the plot:
A group of top class scientists decide to solve the over population and climate crisis of modern world by causing an apocalypse of some sort, then hide in a safe bunker only to come out after it and repopulate Earth. Something goes wrong, the apocalypse is worse than predicted and they can't leave the vault. Centuries goes by and those of them survived (cryogenic sleep? Or simple reproduction?) builds a "weapon", a sort of bio-mechanical virus that strenghtens itself by scrapping metals and adapting itself to the surrounding enviroment, hence how dino-bots and other cyber-animals come to live. Maybe their developement goes south and the scientists are forced to remain in the bunker? Or do they have other projects? Who knows. The timeframe of the game comes, Alloy is the daughter of two scientists from the said vault, escaped because they were contrary to the other scientists plans, but get killed while on the run. Alloy is the only survivor, carring some device left from their parents that contains some kind of information, gets found by a tribe and raised from them.
Fanfiction is over.