In 19th century France, a struggling single mother, Fantine, leaves her three-year-old daughter Cosette in the care of her new acquaintances, the Thernadiers. Unfortunately, Cosette's caretakers prove to be anything but loving, and the poor girl is subjected to repeated abuse and forced servitude. Still, she endures the torment in the hopes of seeing her mother once again. One night, while doing errands for her host family, Cosette is assisted by an honorable stranger named Jean Valjean. After a brief conversation with the young girl, Jean acknowledges her as the type of person he has been seeking and rescues her from the clutches of the Thernadiers. They make their way to a nearby town where Cosette enjoys a new life thanks to her savior. Under Jean's guidance, Cosette promises to help others with her newfound freedom. She pledges to heal the nation, ensuring that no one else suffers her fate. Though the road ahead is paved with tragedies left by the French Revolution, this idealistic girl will not rest until France is freed from poverty and suffering.

Around the the 37th year of the Meiji Era (1904), in the midst of the Russo-Japanese war, the small Japanese army, in need of assistance, uses its special flying (thanks to a benevolent demon) ship, the Amanohara, to attack Russia's major base at Port Arthur (Lushun). Umakai Shintaro, a Russian diplomat originally from Japan, defects and goes to Sapporo to teach at a girls academy. However, that girls academy is not typical—it is on board the Amanohara, and the five girls Shintaro teaches are known as the Raimu Unit—girls with the ability to summon powerful beings to fight for them. Shintaro eventually becomes their teacher and general in battle, and so the six embark on a weird and excessively erotic journey, as Shintaro helps the girls overcome their weaknesses, become stronger for the final stand at Lushun, and also understand the motives of the "Russian Spiritual Corps" that assist the opponent, which, unfortunately, has one member whom Shintaro knew well...

One day, when Remu Mikage is on a video call with his sister, Shiki, who has traveled to the futuristic Okinotori-island Mega Float City for school, she confesses that both the audio and visuals of her are completely artificial. In order to be more efficient in her studies, Shiki has used neural-linked nanomachines to upload her consciousness onto a computer and is storing her physical body in a "body pool." While shocked, Remu is supportive of his sister's decision, until the disaster known as the "Early Rapture" happens. The Early Rapture causes everyone who has uploaded their consciousnesses to either fall into a coma or perish. Remu visits his sister's empty apartment one last time, but is shocked when Shiki arrives at the door. With no memory of her family or past, and being pursued by a violent group of researchers, Shiki and her brother are forced to flee using her newfound power of nanomachine manipulation.

Just as the planet approached its third World War, individuals with superpowers appeared from around the globe to maintain peace. They became the symbols of their respective nations, striving to limit crime and bring evildoers to justice. Teenage heroine Teru "Shy" Momijiyama is Japan's representative in the world of heroes. When a mysterious threat called Amalareiks emerges, Shy must work together with her fellow heroes to stop them at all costs.