At first I was a little confused by the direction of the ending but I get it now, and boy is it sweet. Basically what we're seeing here is Baku pulling off the same plan he always does on an even larger scale.
Every single arc of Usogui goes like this:
He sets stuff up, plants seeds.
He "loses" BIG and inserts a "wedge"
his seeds sprout
and he makes a comeback.
So for this "arc"
First he plants the seeds.
First is the loss where he isn't strong enough, but inflicts a wedge (losing his heart)
Then, he builds up allies after losing (literally the whole story. Now he's obtained kakerou as the strong ally.)
Here's the difference:
Then he takes on the challenge for real, but this time he had to lose twice, because the first time wasn't enough.
This is so that Hal can complete HIS process of losing and becoming stronger for it. And it also removes him from the picture (I assume the doctor presumes Baku is dead.) Even the author pretends he's dead for a second.
But of course he isn't dead, that's all part of the plan.
and NOW, now that EVERYONE has taken their big Ls and came back even stronger, now is the time for the big, big big comeback.
You don't need the details, you've seen Baku work. You know what's going on. It's all plans, ALL THE WAY DOWN>
I drew some MSPAINT bullshit.