That was weird, too. Why can there suddenly be miniature-Gauna inside of Sidonia?! Why are they bearing human minds/memories? Kinda sucked how Kunato was "killed" just like that, too.

I also wonder what Kobayashi´s/The Council´s goal is. You´d think it is their people´s surival, but at several occasions now it felt as if there is a greater/deeper mystery to it all. "The Gauna mustn´t enter Sidonia". Why? Not only have some of them already, but also what if? Sure, it´d do a lot of damage, but you can still fight inside, too.
Makes it feel as if there is some NGE-esque "mustn´t reach Adam"-agenda going on.