In the near future, androids are a commonplace product of the tech company Khaganate Labs. J4K-109 (Jak) was designed to assist in the development of Khaganate's Project Izanagi, a network of Artificial Intelligences intended to improve the ecological stability of the planet and facilitate a harmony between humankind and nature. Jak's key motivation is to make the world a better place for Chris, the teenage daughter of Stephan, the man who created him, who was killed in a refinery explosion right before the story begins. Stephan also designed M32-97I (Tsubaki) whose soul purpose was to investigate and eliminate androids who defied their core programming. One of these androids—the third created by Stephan—was CR1-YL7 (Carlyle) who was designed for labour in the harshest of environments. Carlyle begins a revolt against his human masters after a secret message left behind by Stephan directs him to a mass android grave. Meanwhile, Jak (suspected of having ‘gone rogue') gets arrested by Tsubaki but is freed by Harry Valentino, Stephan's brother. Jak learns that one of Tsukuyomi's AI subsystems (Ares) is vying for control of Khaganate Labs and is systematically eliminating all threats to that control, including all ‘free' androids as well as the other AIs belonging to Izanagi. Jak obtains an AI ‘killswitch protocol' from Kagutsuchi, a failsafe designed to stop any of Izanagi's subsystems from going rogue. He then heads for Ares' mainframe to put an end to this. Tsubaki, meanwhile, has been tracking Jak down, but her investigation has uncovered deleted memories buried deep within her subconscious. She begins to experience guilt, and she questions her purpose. Carlyle (directed by Stephan's message) seeks out Harry and Chris, who point him towards Ares. The three protagonists converge at Ares' mainframe, and Ares reveals that it intends to complete its directive by manipulating the thoughts and decisions of all human beings. A small fight occurs between Khaganate and the 'free' androids, but the androids retreat. Jak learns from the other AIs that Khaganate's original purpose was to initiate something called the Homo Deus Protocol, a plan to systematically replace human beings with a new race of human-android hybrids. He realises that by stopping Ares, he will be ending the human race. Tsubaki, unable to stop wrestling with her conscience, is executed by Khaganate, but she survives and joins Carlyle and the android revolution. The androids assault Khaganate, creating a diversion so that Jak can access Ares and shut it down. Izanagi speaks to Jak, revealing Stephan's master plan: for Jak, Tsubaki and Carlyle to merge their consciousness and create Hana, the first Homo Deus, an immortal replica of his daughter Chris. In doing, Jak must sacrifice his friendship with all of the humans in his life, including Harry and Chris.