When a series of mysterious attacks involving Cogito infected AutoReivs occur, Re-l is assigned to investigate, and encounters a humanoid monster. Later, she is attacked by two of these monsters at her home.

Re-l struggles to convince her peers of her encounters with the monsters, which she learns are called Proxy. She is removed from the investigation and finds that Iggy has had his memories of recent events erased. Meanwhile, Vincent finds himself on the run from a proxy and then the city’s authorities.

Re-l braves the outside world in order to bring Vincent back to Romdo. While there, Raul commences his plan to capture Vincent by attacking the Commune with patrol drones. Re-l’s environmental suit is damaged and Vincent is injured in the attack. Re-l suspicions are confirmed that there is a link between Vincent and the Proxies.

Vincent and Pino stumbles onto war-torn Halos, where they are caught in a war between the dome’s human inhabitants and its autonomous AutoReivs.

Vincent finds a strange book store and an even stranger old man, where he discovers more about his true nature. Re-l and Iggy catch up on the Centzon (the Rabbit, the flying ship that Vincent travels by).

While resting in a long-abandoned dome, strange occurrences take place and the trio’s lives are endangered.

When winds die out, the trio are stranded aboard the Centzon and Re-l finds herself struggling to hold on to her sanity.

Pino explores the mysterious Smile Land with the NaKaMa, and confronts the Creator of the city.

A Cogito outbreak spreads through Romdo and the city falls into chaos. Vincent incites the people to revolt, pushing them to hunt down and kill all AutoReivs.

Pieces are played and revelations uncovered as the final fight commences. Monad makes her return and tries to convince Vincent to join her.