* Near the end of the game [[spoiler: after York kills George and goes to his house. You find some [[ChekhovsGun very familiar red tree saplings.]]]] At that point you find out that [[spoiler: [[TheReveal Kaysen was]] [[TheManBehindTheMan behind the entire thing!]]]] [[spoiler: You might remember at this point that [[OhCrap Emily has disappeared and was with Kaysen last.]] You race against time to try to save her, but when you arrive it's already too late. Forrest used the red seeds and planted a sapling inside her, which has already hatched. She then stumbled towards York, begging him to kill her.]] And the worst part of all? [[spoiler: You have to ''manually pull the damn trigger!'' That's right, you have to force York to MercyKill the woman that he loves.]]
** No, the worst part is that after the game forces you to [[spoiler: pull the trigger, Zach ''still'' can't bring himself to do it.]]
** What Emily resorts to doing to resolve the dilemma is also heartbreaking.
* The epilogue after the FinalBoss fight didn't help much either. It's a very BittersweetEnding.
* Some people thought that [[spoiler: the Raincoat Killer level, with Amazing Grace]] was, in it's own way, poignant and sad.
* Thomas. Just... Thomas. [[spoiler: He's in love with George, who will never love him back, despite being willing to help him get away with ''murder''. It really, really doesn't help that York, the only other person he's attracted to as far as we know, has fallen in love with the ''same woman'' George has. Ouch. Thomas is absolutely crazy by the time you fight him, but it's hard not to feel sorry for the poor guy]].
* George's mother used to whip him with tree branches, and tell him that it hurt the trees more than it hurt him. He believed her, so he used to go out to the forest and apologize to the trees afterward. Poor little kid...
* Sallie Graham's utter grief at the death of Anna, her daughter.
* Harry telling [[spoiler:Michael, his adopted son, that he's proud of him]]. While definitely a CrowningMomentOfHeartwarming, it takes on a sad subtext when you realize that [[spoiler:George wouldn't have fallen to evil had Harry remained in his life instead of abandoning him to his abusive mother]].