All the events after reading Chise's diaries in the last episode occur in Shuuji's mind
Shuuji snaps after reading Chise's diaries at the observatory. He goes insane and hallucinates she is with him in another form. Chise's appearance and non-human form, the weird wing-like plates in the sky, the attack and the tsunami are all taking place in his mind, making the end of the world a symbol of his lost love. The events in the "white world" and the relived memories are merely dreams within dreams. The world might not have ended and Chise might still be alive, but we don't know for sure. As far as Shuuji is concerned, everything is gone for him.
- Probably not true. I mean, the tsunami is symbolic and all but also a very logical thing that could have happened there. Plus, Chise have already grown to gigantic proportions by that point and Shuuji didn't know that. And despite being heartbroken Shuuji wouldn't want for all his classmates and parents to die.
- I actually thought that the whole series was Shuuji's hallucination, that the end segment where he's in the gray with nothing but an energy being (light bulb) was a testament to how he was going around in his cell, talking to himself.
The ultimate weapon is basically the Obliterator virus since it transforms Chise into a mechanical abomination. Heck, one scene has her essentially shit missiles!
The story was set in one of the hive worlds that looks like Japan. And in the end of the series the sky turns red, Chaos approached.
- Ah, this explains why the plot is so incredibly depressing. "There is only war", indeed!
- She doesn't show any of the physical deformities that ought to come with the infection though, not until the very end.
- Hey, Chise could might as well be a Mechanicus Experiment to make an "Imperial" Obliterator virus, after all, the Imperium are Catholic Space Nazis! That could also be why she looks like an Angel of Death!
And those relived memories aren't really relived memories but the new world. Of course this means that while she appears back to normal
she's also still basically in control of reality
After becoming all-powerful, she got bored with being a shy little girl after a while, so she recreated the universe once more with Shuuji as Kyon and several of her other friends as members of the SOS Brigade.
After the war started, the government revived the artifical human weapon project and refined the technology into something more sophisticated before using it on Chise.