Within the domed city of Romdo lies one of the last human civilizations on Earth. Thousands of years ago, a global ecological catastrophe doomed the planet; now, life outside these domes is virtually impossible. To expedite mankind's recovery, AutoReivs, humanoid-like robots, have been created to assist people in their day-to-day lives. However, AutoReivs have begun contracting an enigmatic disease called the Cogito Virus, which grants them self-awareness. Re-l Mayer, the granddaughter of Romdo's ruler, is assigned to investigate this phenomenon alongside her AutoReiv partner, Iggy. But what begins as a routine investigation quickly spirals into a conspiracy as Re-l is confronted by humanity's darkest sins. Elsewhere in Romdo, an AutoReiv specialist by the name of Vincent Law must also face his demons when surreal events begin occurring around him. Re-l, Iggy, Vincent, and the child AutoReiv named Pino will form an unlikely faction as they struggle to uncover Romdo's mysteries and discover the true purpose of the mythical beings called Proxies.

Tomoya Aki, an otaku, has been obsessed with collecting anime and light novels for years, attaching himself to various series with captivating stories and characters. Now, he wants to have a chance of providing the same experience for others by creating his own game, but unfortunately, Tomoya cannot do this task by himself. He successfully recruits childhood friend Eriri Spencer Sawamura to illustrate and literary elitist Utaha Kasumigaoka to write the script for his visual novel, while he directs. Super-group now in hand, Tomoya only needs an inspiration to base his project on, and luckily meets the beautiful, docile Megumi Katou, who he then models his main character after. Using what knowledge he has, Tomoya creates a new doujin circle with hopes to touch the hearts of those who play their game. What he does not realize, is that to invoke these emotions, the creators have had to experience the same feelings in their own lives.

After joining the resistance against the bakufu, Gintoki and the gang are in hiding, along with Katsura and his Joui rebels. The Yorozuya is soon approached by Nobume Imai and two members of the Kiheitai, who explain that the Harusame pirates have turned against 7th Division Captain Kamui and their former ally Takasugi. The Kiheitai present Gintoki with a job: find Takasugi, who has been missing since his ship was ambushed in a Harusame raid. Nobume also makes a stunning revelation regarding the Tendoushuu, a secret organization pulling the strings of numerous factions, and their leader Utsuro, the shadowy figure with an uncanny resemblance to Gintoki's former teacher. Hitching a ride on Sakamoto's space ship, the Yorozuya and Katsura set out for Rakuyou, Kagura's home planet, where the various factions have gathered and tensions are brewing. Long-held grudges, political infighting, and the Tendoushuu's sinister overarching plan finally culminate into a massive, decisive battle on Rakuyou.

Since the death of his parents, Shinpei Ajiro had lived with the Kofune family and their two daughters—Mio and Ushio. Although he then left his home island to continue his education in Tokyo, Shinpei returns after Ushio tragically drowns during the attempted rescue of a little girl. During the funeral, his best friend informs him about bruises found around Ushio's neck, casting doubt over the cause of her death. Suspecting a murder has taken place, Shinpei reevaluates recent events, but strange incidents only continue to transpire. Disappearing people and other unexplainable occurrences lead Mio to recall an old folktale referring to entities called Shadows, which may not be entirely fantasy. Supposedly, an encounter with one's Shadow foretells the person's impending demise. Facing the dark side of Hitogashima Island, Shinpei stands against his grim fate to fulfill Ushio's final will—to protect Mio.