Set in the year 11945 AD, the story revolves around a war between the human-made androids and the machine army of invaders from another world. Lacking both emotions and true names, androids have particular attitudes that distinguish them from their fellow androids. The YoRHa android forces are commanded from the Bunker, a reconnaissance base in orbit above Earth. They fight alongside the pre-YoRHa androids on Earth (known as the Resistance) to drive back the Machines. The initial protagonist is 2B (short for "YoRHa No. 2 Type B"), a YoRHa combat android whose main traits are her calm and composure. 2B is accompanied by 9S (short for YoRHa No.9 Type S), a male "scanner" android who displays more emotion than the other YoRHa units. Eventually another playable character is introduced: "A2", an obsolete attack android with a taciturn personality who often chooses to act alone. The androids are supported by Pod 042 and Pod 153, floating box-like robots that act as ranged weapons. The primary antagonist of the game is the machine network and its creations.
The first and second playthroughs follow the respective views of 2B and 9S during an initial invasion. After opening a route for future missions, they are sent to clear out machine threats for the Resistance, led by Anemone, who provides the two with support. During their missions, 2B and 9S discover that the machines are exploring human societies and concepts. The two work with a pacifist machine group led by Pascal; battle Adam and Eve, physical manifestations of the machine network who reveal that their creators were destroyed centuries ago; and encounter A2, a rogue android on the run from YoRHa. Adam is killed by 2B after he captures 9S. During his recuperation, 9S discovers a glitch in YoRHa's servers when syncing himself and 2B, and learns that humanity was extinct long before the alien invasion. Their last remnant is a Moon-based server holding humanity's incomplete genome remains. YoRHa perpetuates the myth of their survival to maintain morale and give androids a "god" to fight for. With Adam dead, Eve goes mad with grief and drives the machines under his command into a frenzy. 2B and 9S kill Eve to end the rampage, but 9S becomes infected with Eve's logic virus, forcing 2B to kill him. However, 9S's consciousness survives within the local machine network. Thus, the two are reunited once again and the story continues.
After finishing the first and second playthroughs, another playthrough unlocks with an additional three endings that uncover the truth behind the world in NieR:Automata even more. The five main endings aside, there is an additional 19 "joke" endings available as well, representing every letter of the alphabet. These are short and acquired through specific means and are by no means canon to the story.
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