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Tear Jerker: X-Men: Destiny
Pixie's death. A bubbly young mutant who gets captured and used to harvest her powers, then shot down while n a helicopter. If you get to her in time, she tells you that she's not important and you need to stop them using her power. You try to help her out but you're not strong enough, until it explodes and she's killed in the blast. When Cyclops tries to mourn, Magneto refuses to let him because he believes he's responsible for her death. During his boss fight, Cyclops tells Magneto that he loved Pixie like a daughter, and once its all done, he's the one ho carries her boy back. The whole section of the game is pretty sad, especially if you've read the comics and are familiar with the characters enough.