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Tear Jerker: Far Cry 3
If you have a brother, watch the game's opening at your own risk.
Doctor Earnhardt lost his daughter when she was only two. He's constantly high on various substances because he's trying to forget. He even mistakes Daisy for his little girl.
The bad ending where you kill your friends and your own brother. Jason really has gone down the rabbit hole
Liza's begging, man... Too much.
The good ending for that matter also has Dennis breaking in a full aversion to Manly Tears over his accidental killing of Citra. The screen fades out to the sound of him begging her to Please Wake Up
Made even worse that despite your refusal of her ways and the life she has planned for the both of you, Citra jumps in front of that knife and saves your life anyway.
Reading the Letters of the Lost, especially the ones made by the radioman, are heartbreaking. Basically, he had a family in his hometown while he was away. That home town was Hiroshima. He smashes the radio to keep his squadmates from feeling the same grief (also implied to be the loss of World War II), but it ends up dooming them all.
The mission "Light At The End Of The Jungle." A kind, quiet religious woman asks you for help because she can't go to anyone else - she suspects her husband is cheating on her with another woman. She's half right - it's a man. You have the option to tell her, or to confront the husband and convince him to man up and tell her. When Jason asks if he'll stay with her, he looks at the ground dejectedly and says "I've already hurt two people I love. I don't deserve either of them."
An extremely brief one, when Jason tortures his younger brother Riley because he has to maintain his cover. Sam manages to work the camera enough to give them a chance to talk, and Jason immediately does into brother-mode. But Riley's absolutely anguished incredulity when he thinks that not only has his brother finally shown up, but is working with the mercenaries and is torturing his own brother is heart-breaking. The voice actor manages to pack a whole hell of a lot of emotions into one line, and it's tough to bear.
I find Vaas as a whole to be a Tear Jerker. It's implied that he was once a normal(ish) person. A lot like Jason. It is also implied that he was given a choice between his family Citra and power, the ability to kill, drugs and money, which is basically the choice Citra gives Jason at the end of the game. Do you want to save your family, and your sanity or do you want to rule an island?
Take Vaas' last words and Citra's lines in the bad ending into account: at one point, he was being groomed to be exactly like Jason- a saviour to the Rakyat. Except, unlike Jason, there was no redemption for him when he chose his new "friends" instead of the Rakyat- just a long descent into insanity and drug addiction.
Finding out what happened to Keith and seeing how bad Buck messed him up.
One side mission involves finding diamonds for a woman so that she can escape the island (her husband is pimping her out to privateers.)Seems straightforward, right? Well, when you find them, it turns out her husband was setting her up to trick Jason so that he could take the diamonds. he will then start beating her, and the game will prompt you to kill him to save her. When you do, she will be horrified and will start crying over his corpse. She will never move from that animation until you leave, and its a really jarring twist to what seemed like a simple fetch quest.
Occasionally you find bystanders weeping over dead bodies in random places. There is nothing you can do to help them. It really compounds what an utter Crapsack World the Rook Islands are.