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Tear Jerker: Republic Commando
The ending, in which Sev, who you have spent the game growing to like and admire as a badass, suddenly goes silent on the com. Your squad-mates try to go back for him, but are specifically ordered to get out of there, forcing you to leave Sev behind, all of you mourning, no idea what has happened to him, your only comfort that you've set the stage for success on Kashyyyk... and even that is tainted by the knowledge that the Republic you've been fighting for, the Jedi giving you orders... all of it is due to end so very soon.
And add to that that the one who is most broken up over the loss, to the point where he's almost prepared to mutiny, is Scorch. Scorch and Sev had the most antagonistic relationship of any of the characters in the game, and suddenly you realize that it was actually the sort of affectionate joking that only someone who is close to their brother or a brother-like figure knows.
And just to twist the knife: we'll never know what happened to Sev or the team, since Karren Travis has moved to Halo, and LucasArts has no plans to continue it.
LucasArts is gone now, too. Traviss wrote a novel detailing the eventual aftermath of the mission to Kashyyyk, though. Sev was never found in spite of search and rescue attempts by both another commando squad and Delta squad's training sergeant himself coming to look for Sev on Kashyyyk, and Scorch, previously the friendly, lighthearted goofball of the squad, becomes a bitter, angry, and disillusioned man whose brotherly bond with his squadmates becomes irrevocably strained.