NieR: Automata | YoRHa Commander SPOILER!
When 2B and 9S return to the Bunker to report the logic virus attack on the YoRHa units on Earth, the Commander does not believe them. Instead she accuses them of irrational behaviour and orders them detained on suspicion of virus contamination. Before the YoRHa infantry can apprehend 2B and 9S, they all break down with obvious signs of the virus affecting them as well. 2B and 9S fight them off and grab the Commander to safety.
As the three of them run to the hangar to escape the Bunker, the Commander stops dead in her tracks and states that she is remaining there. As she opens her eyes, the glowing bright red light indicates that she too has been infected with the logic virus. 2B’s plea to allow 9S to hack the Commander to purge her of the virus proves futile as she is firm on fulfilling her duty to the end. She then orders 2B and 9S to survive as the last remaining members of YoRHa.
9S drags a sorrowful 2B to their Ho229 Flight Units, leaving the Commander behind to self-destruct the Bunker as they flee for good, never to return. The Bunker and its inhabitants are officially dead.
2B and 9S are separated on their descent to Earth and due to her prolonged exposure to the infected YoRHa units, the virus spreads to 2B’s system as well. She instructs Pod 042 that she needs to find a secluded area to go to in order to prevent the virus from spreading to any other android when her body eventually fails.
Platform: PlayStation 4
All © copyrights belong to their respective owners, Square Enix Co., Ltd. & PlatinumGames Inc.