6. Rise, Forsaken - World of Warcraft
Both the Horde and the Alliance have their fair share of morally questionable missions, but "Rise, Forsaken" has to take the cake as the one that will truly have you asking: "Are we the baddies?"
The quest is given to you by Sylvanas Windrunner, the Banshee Queen of the Forsaken, who orders your character to kill a group of human refugees hiding on an island and then resurrect their bodies so that they can become a part of the Forsaken army.
If this already doesn't sound like the most twisted scheme ever, the refugees you fight will try to run away from you and get progressively more desperate about trying to preserve their lives. The mission even ends with the refugees drinking Worgen blood and becoming cursed, just so that they can be spared turning into the undead.
To add more guilt to your actions here, the process of killing and raising innocent refugees is exactly what the Lich King used to do and what Sylvanas and her Forsaken are supposedly against.
This means you aren't just a monster for completing this quest; you're a hypocrite.