Yup. So the solution is not to make your villain a superintelligent god with a horde of bloodthirsty nanobots, the invincible Elder Lightsaber, and the One Thing to Rule Them All to begin with. Eliezer took the risk of setting up an incredibly powerful villain, and it is to his credit as a writer that up until the very end he made us believe that he was capable of writing a satisfying resolution anyway.

Frankly, he still might. There are four chapters left, and Eliezer is nothing if not capable of surprising his audience. And as a Naruto fan, he might also have come across Bleach (another of the Big Three shounen series), and learned from its author already having made the exact same mistake.