Part of it is just a serious structural fault in the show.
First off, by this point, we already had the comic's ending in which Jack defeats future Aku and works to make the future a better place post Aku.
Then, we had the first three episodes selling this season as a more mature, grimdark take on what came before.
Then, over the course of the next few episodes, we get a whirlwind romance of former blood enemies, because the only one he didn't kill just happened to be the one that was fascinated by the world outside her training to kill the samurai.
And, with the finale, we have so much wasted time, that it's practically a joke that it wraps up the plot as quickly as it does.
The problem is, it needed at least two more episodes, with the final battle being a two parter. But Gennedy himself only wanted ten, but clearly didn't plan anything out.
Likely, the guardian being dead was simply something thrown in because someone reminded him of that episode midway through the production. Same with how it all ended in what must have been an early, quick draft of the episode at which point he must have just thrown up his hands and said end it.