Well Cereberus certainly doesn't care about looking like the good guys anymore. Dark helmets with slanted red eyes don't exactly scream "protagonist".
Quiet Stranger said:
Okay so everything I've done for cerberus, I shouldn't do? In case it comes to bite me in the ass in 3? Like saving the reaper technology or letting that scientist guy continue to experiment on his brother?
If you did that you're a pretty bad person to begin with imo.
Honestly, how anyone could want to hand reaper technology over to the Illusive Man is beyond me.