When the useless side character turns out to be the final boss

Marx (specifically the one from Kirby super star) all he does is tell Kirby to go wish for the sun and moon to stop fighting. And then he betrays Kirby after he gets to Galactic nova and wishes for ultimate power.

Firth from Another Crab’s Treasure. He steals the heart of the ocean after Krill (the main character) kills the jellyfish guarding it after not doing anything the whole game.