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Tear Jerker: Transformers Energon
Demolishor sacrificing himself to save Megatron. The fact that the title of the very next episode reveals that he gets better doesn't diminish the drama of the scene, especially in the original Japanese.
It actually gets sadder when Demolishor is brought back to life... as an idiot disgracing the original.
Poor Alpha Q! All he wanted was his home planet and Scorponok back.
Starscream is revevied! Hurray! ...oh wait, now he's a mind-controlled zombie for Alpha Q. But wait! he's free ...oh, now he's Megarton's mind-controlled zombie. Sometimes life just plain sucks!
And it wasn't just simple brainwashing, he had his personality reformatted to be passionately loyal and devoted to Megatron. His Undying Loyalty actually makes him outright sympathetic at times, especially when he decides to face his fate alongside his master.
Poor Inferno goes through almost the exact same torture as Starscream but unlike Starscream he manages to overcome it. Only to be killed moments later, thankfully his fate turns out to be a happy Tear Jerker in that he is revived shortly after.
In the final episode Optimus (and pretty much every other Autobot) vows that he's not going to let Galvatron/Unicron go. Turns out Optimus and the others plan on commiting a Heroic Sacrifice in order to stop the chaos bringer. But just then a familiar voice speaks, and Galvatron's eyes return to normal; in control of himself again, he hurls Optimus aside. He then smugly proclaims to Unicron that though he may be inside him, he will never possess him. And finally, with a cry of glory, Galvatron plunges himself into the plasma sphere and dies... Perhaps not as emotional as his "Armada" death, but it still manages to make your eyes sting a little.