I know that was supposed to be intentionally unclear as to what happens, but I'm not sure if what I'm misunderstanding was meant to be misunderstood.
Nike murdered the mother before leaving, but what was that thing on the right side of her head? It looks like the bomb being dropped on the last page, which makes me think it wasn't a nuke but an alien bomb being sent in. In which case we could assume the DNA Nike took was from Ai, and they merged, making it a pseudo-happy end.
Alternatively, the device could have been what was need to extract DNA and it sucked out the mother's brain or something (which would kinda justify the response to the aliens as a whole) and Nike used that to carry out Ai's wish (she might or might not have been alive during and after this). In this case, the ending is notably more depressing as it implies both Nike and Ai(?) were nuked.
Still not sure what's up with the butthole.