While providing security detail in an unnamed African country for its prime minister, N'Mani, Maverick operative Raiden and his team are attacked by Desperado, a rogue PMC involved in terrorism. While Raiden fends off Desperado forces, their leader "Sundowner" manages to kidnap and execute N'Mani. Sundowner's comrade, Samuel "Jetstream Sam" Rodriguez, fights and defeats Raiden, severely damaging his cyborg body. Raiden survives, and Doktor later gives him a new black cyborg armor that grants him much more power.

NieR: Automata tells the story of androids 2B, 9S and A2 and their battle to reclaim the machine-driven dystopia overrun by powerful machines.