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Tear Jerker: The Legend of Zelda: Phantom Hourglass
The final battle. It looks like Link and Tetra are about to get all of their life-force sucked out of them by Bellum for good, but suddenly, Linebeck, of all people, starts to fight the monster off. This must be the hugest character development in a Zelda game EVER! (Not even Midna managed to change her ways that much). After all you've gone through so much alongside this Jerk with a Heart of Gold, he's finally proven that he's more than just a selfish idiot... and suddenly, Bellum comes up, possesses him and transforms him into a monster himself. Your only choice is to fight him, right after he got his Moment Of Awesome. Even made worse by the fact that he weakly calls out to Link, just before the transformation is done.
It's even better in the (little known) manga, where he almost commits suicide to stop Bellum, and it takes a time sphere to stop him! And then as he holds the sword to his neck, he tells Link that he really did like travelling with him, and tells Link to grow up to be a better adult than he ever was.
When Link finds Tetra turned to stone, his expression is heartbreaking.