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 Properly Paranoid by that point he thought it was the First Sons and fled.
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. 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".