When a poisonous rain of Xistazul fell from the sky, humanity took refuge underground to escape the deadly tragedy, known as the Tears of the New Moon. 100 years later, people returned to the surface to begin a new era. With the constant threat of the Eliminators, the humans created settlements, called Nests, alongside humanoid AIs, called Magus. In 2242, Kanata dreams of becoming a nomad. While exploring the ruins of a museum with the renowned Tokio Nomad, he meets a Magus called Noir, who has lost all her memories. Noir struggles with everyday tasks, but shines in a battle against the Eliminators. Kanata joins Noir as she discovers what it takes to be a Nomad.
The year is 5012. A sudden invasion of aliens and their Mechanical Living Beings almost wipes out humanity entirely. The few survivors take refuge on the moon, organizing a counterattack to retake the planet, but come to a standstill due to the infinite multiplication capacity of the Mechanical Living Creatures. To break the deadlock, humanity creates YoRHa, a unit of android soldiers. 2B, an android, is sent to Earth to meet 9S and analyze the mysterious phenomena they find there.
Awakening in a strange virtual world with memories of the past, Hakuno finds himself forced to fight for survival in a war he doesn't understand for a prize beyond value; the chance to have his wish granted. With only an enigmatic "Servant" at his side, Hakuno Kishinami will have to face friends and enemies in battles to the death in order not only to gain possession of a mysterious object known as the "Holy Grail", but also to find the answer to the most important question of all: "Who am I?"