Many thought-provoking and disturbing things happen in the game. There is one which for me completely stands out. Samara's loyalty mission. Read, talk, listen to everything, get to know Morrinth's victim. Feel her mother's pain. Then go play with Morrinth. Talk to her as much as you can, learn how truly f@#$ed up she is. Then choose her over Samara. 100% renegade, nothing really wrong with it, right? You decide she's more useful for your missoin so you pick her.
Go back to the Normandy, talk to her. She's so non-chalant about the whole thing and it's easily obvious she's going along just so she maybe gets a chance to consume you as well.
Now go about your business. Check your mail like you always do. Oh, a message from that girl's mother.... You already totally forgot about her, right? She thanks you for doing justice...
THAT broke me. I never ever felt more evil and disgusted with myself in a game before. A 100% renegade means you do stuff which in a more normal situation would be considered evil, but hey there's a galaxy at stake so anything goes. I could always come up with some justification for my actions. Hey, a little collateral damage here and there, big deal. So what if I was a little more cruel to random mercs than necessary. But this, no, this was real evil.
Choosing not to send anybody to escort the crew comes close, but at least they voluntarily went on a suicide mission.
That's why I love playing renegade in ME. Paragon is so straight-forward it's boring. Paragon is what "normal people" are expected to do. Paragon is having a good end goal and going after it in a good way. Renegade on the other hand, you still have the good end goal but you do evil to get to it. It's so controversial it makes me actually think about everything that happens and whether I'd really make the same choices in real life.