In the end, Aphrodite realises she can't love Marcus in his current state of mind.

A furious Marcus orders that the attack continue until they are all wiped out, then he gives command to one of his men. The plan for the gen and cyborgs was never to see who is strongest, but who is easiest to rule over. Meanwhile, the IXs Mother orders that the gen city be destroyed as well. Aphrodite asks Marcus to stop killing the civilians, but he is blinded by his religious fervor. Marcus's assault on the cyber city is in full swing, aided by the guards being in disarray from Ares' previous attack. He recovers Aphrodite to fulfill a plan to destroy the world and remake it in their Mother's image, the woman Aphrodite refused to kill in the very first arc. Aphrodite is restrained and the cyborg council decides to put her in stasis, but Ares IX attacks using his android clones, the XVs. It's revealed that there are nine IXs in total, all trained by Burch and seven of them are banded together. The latter was controlled by another IX model. They infiltrate the cyborg facility to find Burch, but he reaches Aphrodite first, right after an impressive, but one-sided fight between her and a mind-controlled XV. It turns out that XV was only testing her and then she is take to what XV calls Sanctuary VI, an underground vault where several more Aphrodities await activation. Meanwhile, an exiled Aphrodite is being hunted by another Aphrodite, model XV. He has become like a messiah to them, uniting the tribes and building an army against the cyborgs. There is more focus on the religious aspect of Marcus's faction. Another faction from Aphrodite's past rises in this arc and it is capable of a great deal of destruction. The war between the gens and cyborgs becomes bloody at the end, but it is far from over. They created several different species in an attempt to make sure some survive and the two warring factions on the surface aren't the only ones still alive. The cataclysm that created this world was predicted by the humans of Aphrodite XI's past, hundreds of years ago.

We are given more insight into the Earth's past.

Aphrodite ix rebirth