* Zelda's capture in this game; it's clearly not enough that she gets TakenForGranite, ''ohhhh no!'' Let's have Link stand in front of her, trying to protect her, then getting [[CurbStompBattle completely pushed aside by Vaati]]. If Link could show emotion in a 2D environment, he'd be past the DespairEventHorizon by now...
** Saying nothing of what happens near the end of the game; at a certain point, [[spoiler: Vaati starts draining Zelda's life force as you fight through the last hordes of enemies, with a bell chiming three times before the process can be complete. If you don't stop him before the third chime, Zelda will have all of her life drained, leaving her as a lifeless statue...thank Hylia it's not the canon ending.]]
* [[spoiler: Ezlo has to return to his home dimension, presumably leaving Link forever]].
** ''"It suits you... little hero."''