* [[spoiler:Trish's death. [[MortonsFork No matter what you do, Cole can't save her.]]]]
** [[spoiler:In the evil version, it's even more sad because she dies hating you and what you've become. Not the best way to go.]]
* If you collect all the Dead Drops, it's revealed that the chopper trying to pick up John when he and Cole first met really was from his agency, trying to pick him up and bring him home. He was so ProperlyParanoid by that point he thought it was the First Sons and fled.
** Way I read it was they felt there was no more Jack could do as Kessler had already succeeded in his terrorist attack and were pleadingly asking him to come home (which would explain why he wasn't getting further support or communications), but he's unable to let go and pushes on alone.
* The end of the first mission has Trish breaking up with Cole after learning that he opened the Ray Sphere, resulting in the death of her sister.
* The good ending. [[spoiler:Cole realizes that everything he had been fighting for is a lie and that's he unsure of what will happen once he fails to be there for empire city. He also reflects on the fact that Moya's still planning "God knows what'", that he's also unsure of Zeke and that with Trish dead he concludes "I've never been more alone".]]
* On the final day Cole wakes up in the Historic Centre park, and you realise he's been sleeping next to [[spoiler: Trish's grave]].