What is a story were the main villain actually turned out to be the good guy?

It’s important to remember that the Quarians are living in the shadow of a war and exodus they didn’t personally start and have had generations telling them a story of survival and heroism against an unstoppable machine juggernaut. That’s what makes their decision to cooperate all the more powerful. They’ve spent their whole lives trying to plant a tree whose shade they’ll never sit in that they always feel is at risk of being cut down again.

It’s also understandable when a significant portion of the geth just tried to kill everybody a few years prior and was abducting humans to impale on spikes that turn them into machines-monsters.