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Tear Jerker: Kid Icarus: Uprising
Chapters 18, 20 and 21. Why?
Chapter 18 is the Wham Episode, when you learn that Pit's soul and conscience has been trapped in the Ring of Chaos for three years with his mindless body slaughtering people during that time, and Palutena has been possessed and become the enemy of mankind .
Throughout the chapter you fight Centurions, who in Chapter 17, declared they'd be happy to die for his sake, and now they're trying to kill you. Someone give Pit a huge hug.
Chapter 20 has Palutena getting impaled by the Chaos Kin's tail and having her soul ripped out in front of Pit's eyes, just after he thought he saved her, and she turns to stone.
Chapter 21 After Palutena's soul is recovered and goes back to normal, the Chaos Kin's remains attack Dark Pit and send him falling to his doom. Pit then demands to Viridi to activate the Power of Flight to save Dark Pit from the Chaos Kin, knowing full well that his wings will burn up. After he saves Dark Pit and the goddesses recall them, we get a gruesome shot of Pit's burned wings, complete with exposed bone and blood, and for extra emotional impact, Palutena recalls Pit wanting to fly on his own.
Palutena: Oh, Pit...
Also, if you fail to shoot down the Chaos Kin, Viridi tells Pit that he's out of time, she can't extract him, and that she's sorry. It's how sad she sounds that makes it a Tear Jerker.
In Chapter 20, you can kill Palutena by shooting her instead of the Chaos Kin. Fortunately it's a game over, but Pit's "What have I done?" makes it that dark.