NieR Automata: Story & All Endings Explained
Part Three: The Last Surviving Members of YoRHa
2B and 9S are sent back to Earth once more to help in the war against the machines. The pair is tasked with acting like a guerilla unit, providing assistance to any YoRHa androids who need it. However, the YoRHa androids are quickly ambushed by a group of machines, and they’re knocked unconscious by an EMP attack. 9S, who has been providing support from higher ground, quickly hops down to protect them from the incoming machines. As the machines gather round for a final push, 9S quickly hacks into 2B’s systems to help her regain control over her own mind and body. However, it’s too late for the rest of the YoRHa units. The remaining members are infected with some sort of logic virus, causing them to turn against 2B and 9S.
The pair quickly escapes from the area, but find themselves surrounded again. With no other choice left to them, 9S tells 2B that he’ll upload their memory data to the Bunker, and they can wipe out the YoRHa androids here via a black box reaction that would destroy their bodies too. The initiate the self-destruct sequence, and 2B wakes up in the Bunker moments later.
2B finds 9S in the hallway, and they quickly go to tell the commander what has happened. However, the commander doesn’t believe them, stating that she received no report about a logic virus and that she didn’t order a retreat either. Just as the commander orders for the arrest of 2B and 9S, the YoRHa androids around her are revealed to be infected with the virus too. 2B and 9S then protect the commander while fighting off the infected units. As the three of them try to make their way to the hangar to escape, we can hear the infected units laughing and making mention of a flower – another reference to the Cult of the Watchers and the parasitic Flower that started it all in Drakengard 3. When the commander asks how come 2B and 9S weren’t affected by the virus, 9S mentions that he’d actually deferred their memory data to the Bunker through another route to be safe, and that was probably why they were okay.
Once they reach the hangar, the commander stops in her tracks and says that she can’t go with them. As she opens her eyes, we see that they’re red too, revealing that she’s been infected by the virus as well. 2B and 9S are then forced to take their flight units and escape as they watch the Bunker explode right in front of their eyes, along with all their fellow androids from the YoRHa unit. As they make their descent to Earth, they’re pursued by infected YoRHa units. 2B takes over 9S’ flight controls and puts him on an auto-pilot route to get him to safety.
2B crash lands at the Flooded City, where she’s attacked by machines. As she tries to move to regroup with 9S, we find out that the virus has been spread to her systems as well, likely due to her prolonged battle with the YoRHa units in the air. She tells Pod that she needs to find a secluded area to go to, so that the virus wouldn’t be spread to other androids when her body eventually fails. 2B drags herself to the commercial district, where she’s ambushed by more infected units. Before they can completely wipe her out, A2 shows up and fights off the infected androids.
On the brink of death, 2B hands over her sword to A2, telling her that it contains her memories. 2B then pleads with A2 to take care of the androids, and tells her that the safeguarding of the future is now left to her. At the same time, 9S locates 2B and starts moving to her position. He reaches the commercial district just in time to see A2 stab 2B with her own sword. Just before she dies, 2B sees 9S in the distance and calls him by his nickname “Nines.” Before 9S can do anything else, there are ground tremors and an earthquake occurs, causing 9S to lose his balance and fall into the Forest Zone. A large white tower appears right in the middle of the City Ruins.