Two years have passed since the events of the original Jinki saga, and Ryohei Ogawara awakens in a hospital stripped of all memory, including his own identity. Desperate to piece together his past, he travels to Kyoto where he encounters members of Angel, a mysterious organization that offers him shelter and a place to stay. There he finds himself sharing a home with three women—the warm-hearted Aoba Tsuzaki, the enigmatic Akao Hiragi, and the antagonistic Kanae Mitsumiya—and begins to settle into what seems like an ordinary domestic life. His fragile sense of normalcy shatters, however, when he discovers the existence of colossal humanoid war machines known as Jinki, forcing him to confront a dangerous reality that may hold the key to his lost memories.