In a futuristic world almost barren of life, mankind is confined to mechanized domed cities where A.I.’s control all aspects of life. In this world, humans are no longer born, they are manufactured in a production line; and alongside them live androids known as autoreivs. Within one of these domed sanctuaries named Romdeau lives Re-l Mayer, one of a few citizens who aren’t entirely prevented from thinking. Her grandfather's prominent position and the affection of the scientist Daedalus have left her more free will than is normally allowed, but Re-l has started to question the sanctity of the city and the citizens' perfect way of life. With mysterious beings known as proxies causing havoc and a man named Vincent causing great influence on her life, Re-l must travel outside of the city to find the answers she seeks and discover the mystery behind "the awakening".
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.
Romdo is no longer a safe haven for Vincent. He is trying to avoid capture by the authorities. As he flees he comes across the infected AutoReiv Pino. Pino then shows him the way to escape from Romdo to the outside world. Re-l struggles to contact Vincent and uncover the true nature of his involvement with the Proxy.
Vincent and Pino are taken in by a small commune, the inhabitants of which make a living off the refuse dumped from the Dome. Meanwhile, Raul plans his move to locate and capture Vincent.
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.
Re-l’s life becomes endangered when she falls ill after exposure to the harsh environment. Hoody hatches a cunning plan to trick Raul and return to Romdo. Quinn leads a group on an escape from the Commune using the Rabbit.
Re-l recovers from her illness. Daedalus shows her the disturbing mechanisms responsible for the Dome’s continued survival. Vincent makes his way home, slowly losing his companions along the way, ending up alone with Pino. A group of infected AutoReivs is unleashed on Re-l, Iggy, and Daedalus. The episode ends with Daedalus filling out Re-l’s death certificate.
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 is introduced to a man named Hauer, and learns some truths about Halos and Proxies, discovering a horrific revelation.
Disturbed by recent events, Raul questions the future of Romdo. Meanwhile, Re-l and Iggy explore a strange antiquated dome inhabited only by primitive 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).
The group is confronted by a vagrant Proxy and its companion AutoReiv, and Re-l puts her new weapon to use.
An infected Iggy becomes enraged and kidnaps Re-l, setting out to kill Vincent. Re-l is again confronted by the homeless AutoReiv.
While resting in a long-abandoned dome, strange occurrences take place and the trio’s lives are endangered.
Finding himself in a bizarre live game show, Vincent’s trivia knowledge is put to the test as he battles for his life.
When winds die out, the trio are stranded aboard the Centzon and Re-l finds herself struggling to hold on to her sanity.
Romdo is on high alert as they search for the fugitive Raul, who plans to activate a deadly weapon. Meanwhile, the trio discover strange humanoids living inside a toxic cave system.
The trio reach the devastated Mosko, Vincent’s home city, and find that the truths lead back to Romdo.
Pino explores the mysterious Smile Land with the NaKaMa, and confronts the Creator of the city.
Vincent finds himself trapped within Re-l’s consciousness, and observes powerlessly as events unfold.
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.
As the city continues to crumble, Vincent and Re-l encounter Proxy One. Raul is overcome with regret and despair, and sets out to find Pino.
Pieces are played and revelations uncovered as the final fight commences. Monad makes her return and tries to convince Vincent to join her.