the aliens genuinely want to help mankind, but obsessed, hyper conservative/ paranoid individuals wage a fairly successful guerilla/ terror campaign against them. eventually, the aliens see their goal as no longer trying to aid humanity, but as essentially stabilizing them so that the radical elements of the earthicans don't spread to other parts of the galaxy/ they now really want revenge on the fucking shit heads. Even though most of humanity isn't at fault, they get bombed to shit and shot etc. and it's all a metaphor for the iraq war.
Alternatively, a setting I'm working on:
Alien life is fairly common in the galaxy, and it's a fluke that we didn't get noticed earlier. Alien life is also incredibly imperialistic, violent, and self serving. The state of the galaxy is basically central park at midnight. Aliens invade and take humans as slaves. wave after wave of various species see us as a convenient source of cheap and expendable labor. However, unlike the other innumberable species who suffered the same fate and eventually went extinct due to being both over slaved and being underdeveloped, humans survive and thrive. human slaves are decently common throughout our general region of the galaxy and not unheard of even all the way on the other side. And we thrive. developing secret languages, secret ways of sharing the past. a network of man yearning for freedom. Until one day, a much bigger bully shows up in the yard and starts kicking the shit out of the individual races, incorporating their slaves slowly. finally, mankind rebels, united at last, and brings about a galactic scale war of liberation for the downtrodden slave races.