The story takes place thousands of years in the future, when mankind has long left the Earth, which is now called Lost Jerusalem, and founded a star empire. The main threat humanity has to face is the appearance of a super-powerful alien race called the Gnosis. The story picks up just after the concluding events of the first episode. Shion Uzuki, the young engineer who designed the powerful android KOS-MOS, arrives with her friends at the planet Second Miltia. They aim to learn more about the heritage of the late genius scientist Joachim Mizrahi, and foil the schemes of the mysterious antagonists Albedo and Margulis. Jin Uzuki, Shion's brother, who was only mentioned in the first chapter, becomes an important controllable character in the second episode. Much of the plot's content is dedicated to exploring the past and the origins of Jr., as well as his connection to Albedo.