2B and 9S are attacked by a group of virus-infected androids on their way to safe ground. 2B reflects on how much she loves 9S and how difficult it is for her to keep having to kill him over and over. To protect him, she takes control of his flight unit and sends him to safety, ready to sacrifice herself.

9S is unaware of 2B's inner struggle and the reasons behind it. He loves her too and hopes that one day she will call him "Nine." He hacks into the autopilot system and returns to the battle, but he is too late. 2B is severely damaged, and 9S falls from the cockpit. 2B tries to hold onto him but plummets into the abyss.

After their reactivation, 2B and 9S find themselves far apart: 2B in the ruined city, missing an arm, and 9S in the desert. While 2B fights hostile machines and her virus infection worsens, 9S searches for her and battles giant machine caterpillars in the desert. The virus spreads rapidly through 2B's system, and by the time 9S finally finds her, she is already severely weakened.

2B is attacked by two infected soldiers and can barely defend herself. At the last moment, A2 saves her, but it is too late to save 2B's life. Resigned, 2B transfers her memories to her sword. When 9S arrives and crosses the bridge to her, he sees A2 impale her with the katana, transferring the memories to A2. 2B removes her mask, smiles at 9S, and calls him "Nines" for the first and last time before she dies.

After her death, A2 cuts her hair and takes 2B's place. 9S, devastated and filled with vengeance, is halted by the collapse of the bridge during a massive earthquake, which reveals a mysterious structure rising from the ground.