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Originally Posted by Nachtwandler
I actually would have prefer such an ending just as it fits the story more.
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Actually, I think this way fits the story more. From the very beginning, the school has been kind of civilization's anchor. It's the girls' physical refuge from the apocalypse. It's Yuki's emotional refuge that she runs to in her mind. It's where they have to go back to in order to find the cure. So it makes sense that it would also be where Yuki would go to do her part in building the world again.