In Episode 24, A2 fights against a virus-infected 9S whose limiters have been deactivated. Despite his enhanced state, A2 manages to defeat him thanks to her tactical skills by severing his sword arm. Unfazed, 9S hacks into A2's system and summons avatars of her dead comrades to hold her responsible for their deaths. With the help of Pod 042, A2 overcomes this psychological attack by focusing on the positive memories of her YoRHa unit, the Resistance, and their brief alliance.

After freeing herself, A2 asks Pod 042 to repair 9S. The machine lifeforms announce the end of their conflict with the androids. The tower, once a weapon aimed at the moon server, turns out to be a launch vehicle for an ark designed to carry the collective consciousness of all machine lifeforms to a new world. A2 activates the launch mechanism, and as the tower collapses, she is buried beneath the rubble.

During the credits, glitches occur, and the scene rewinds to a void where Pod 042 expresses dissatisfaction with the outcome to Pod 153. Pod 042, having developed self-awareness and emotions through interactions with 2B, 9S, and A2, refuses to accept the end of the YoRHa project, which mandates the destruction of all data and hardware. The pods rescue 9S but face resistance from other pods that still refuse to accept the project's conclusion. Pod 042 and Pod 153 join forces to destroy them.

As a result, 9S and 2B are restored and awaken without their blindfolds. 2B greets 9S with "Good morning" and calls him "Nines," as she once did. Freed from the war and the YoRHa project, they can now live together in peace. Meanwhile, A2 is repaired by an unknown woman with glasses, who winks at her before disappearing.