Well quite a bit happens. At the end of route A both Adam and Eve have been killed and its happily ever after. Route B starts with you doing the story over from 9s' perspective. This unlocks the hacking mehchanic for the game which was probably my favorite part of the game. 9S being a high end model eventually discovers that the humans long ago died out and that Yorha simply created the illusion that humans lived on the moon. This route ends the same way A ends. Route C/D starts and everything goes to shit. Yorha launches an all out attack on earth to end the machine threat but during the attack the entirety of Yorha is infected with a logic virus driving everyone hooked up to the server mad. 9s and 2B were not uploaded to the server because earlier the A/B route 9s halted the sync process when he was undergoing maintenance after sustaining massive damage. The bunker is destroyed and only 2B and 9s are left to deal with several maddened yorha units. 2B sends off 9s in a flight unit while she uses herself as a distraction to lure the maddened yorha units. While alone she starts to malfunction and realizes that at some point she was infected by the logic virus and starts to deteriorate. She looks for a place far from androids to prevent spread of the virus. She is eventually discovered by A2 as she neared system shut down and was killed out of mercy by A2.
A giant structure appears out of the ground which is apparently hosts the amalgamation of the machine network. 9S driven by grief seeks to only destroy the network. It is discovered towards the end of the game the purpose of Yorha. It was designed to be destroyed (as only high level yorha knew that humans were dead) so that androids would never find out that humans were extinct (and lose all reason to live.) 9S is pretty much driven mad by all this news. In the end, A2 and 9S face off (you choose who to play as but in both endings A2 dies. In one 9S also dies.) Route E/F can be started after watching the credits once and a POD who has been watching over the androids somehow manages to gather the data of all 3 androids and puts them back together with their memories intact.
There's more details on the C/D ending but i didn't feel like writing it all out. ---