Mass Effect 2 has some great missions within the original game, but I have to say that the Overlord Pack is hands down the most disturbing mission I've ever seen. In a completely good way. In most missions you have the 'Paragon' and 'Renegade' options, and usually you choose the one that gives you the points you want in order to gain enough points to either charm or intimidate.
Sometimes the Renegade option is simply pragmatic rather than just pure 'dickhead,' and the Paragon options are often 'idealist' options. Sometimes, choosing to be a Paragon is choosing to be a Pollyanna, and you say to Shepard, "Yeah, cause that won't come back and bite us in the ass."
Oh wait! Joker actually did say that to Shepard after one particularly interesting mission where I personally think both choices deserved Renegade points. (For anyone who has played the game - I am referring to Legion's loyalty mission.)
There are few missions where you really feel any sort of emotional impact regarding your choices. A few loyalty missions perhaps (Legion's and Garrus' come to mind). But really, there are few missions that actually go so far as to disturb.
The Overlord Pack changed that. I can't imagine choosing a Renegade ending for this mission, no matter how I was playing the game. You play through four different outposts wherein a rogue VI (Virtual Intelligence) is sending every machine, turret, droid and geth after you to try and kill you. By the time you reach the main facility, all you really want is to destroy the damn VI.
Until you see what the VI really is.
It's not really a surprise. Doctor Archer - the head researcher for Project Overlord told you that it was his brother David that somehow merged with the VI and went nuts. But the story he told you when you first met him is not quite the truth, and you totally have a Liar Liar Pants on Fire moment.
Project Overlord is a project to create a VI to be a sort of countermeasure to a geth invasion. The idea is if humans create the right sort of VI, the geth will obey it. Sounds great on paper, right? Well, Doctor Archer decided to use his autistic brother David, by inserting him into a machine. Physically. When you see poor David, his eyes are held open ala A Clockwork Orange, he's got tubes jammed down his throat and wires fed into his limbs. He's crucified and hanging, conscious and screaming, "Quiet,...Please make it stop."
I have to tell you that it was the most pathetic thing ever. And I thought it was brilliant because, despite every game trying to make me feel something and move me, this is the one moment that actually did.