Are the villains Lombaxes?
It does show, i've been playing R&C since 2002.Ratchet and Clank was among my inspirations for this comic (awesome game BTW), so it does show a little I admit. In short they're two villains are the waring factions; imperialist invaders on one end and religious fanatics on the other. I leave a detailed synopsis in the "About this Project" if you want you can get a good gist of the story here kck.st: Tokai.
Though It not my official lore, the aliens in Tokai (they're called the Oma) are a bit xenophobic and they don't like Lombaxes much.