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 he was being used, also that he is not leaving his friend betrayed him and his girlfriend is dead. The part that takes this home is last quote: "I have never felt so alone".