5. Illusive Man (Mass Effect 2)
The Illusive Man is my favorite video game villain of all time. I actually took his side form the most part of the second game. In the third game, he took it too far by fighting the organics as well in addition to the Reapers. So much for pro-humanity right? Like Saren, it's quite obvious that he was indoctrinated and there's even video footage that shows he was. He reveals his plans that it's better to control the enemy than destroy them.
Then you drop the bombshell: THEY ARE CONTROLLING YOU ILLUSIVE MAN. His mind is blown and you can bring him back to reality by reminding him that this is not the way. Consequently, he commits suicide to stop the madness he has befallen.