Gohma from Wind Waker. It was one of the hardest bosses in the game, and it didn't help that you only had 3 hearts (unless of course you got the 4 available Pieces of Heart, but you'd still only have 4 hearts). The second phase of the battle had an unseasonably high level of difficulty for a first boss. I wouldn't say it was extremely difficult, but just not the normal easy first boss that we fight in most Zeldas. And, in comparison with the rest of the bosses from Wind Waker, its difficulty just didn't fit in.
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