Mikoto Misaka and her friends are back, investigating rumors across Academy City. Soon, Mikoto discovers something terrifying: horrific experiments are taking place throughout the city, involving the murder of thousands of espers. Moreover, these espers are far from just ordinary people: they are clones of Mikoto herself. Feeling responsible for their treatment, she sets off to put an end to the experiments; however, the forces opposing her are much more dangerous than she anticipated, and Mikoto finds herself up against some of the most powerful espers imaginable. Toaru Kagaku no Railgun S continues the story of the Railgun as she desperately fights to put an end to the inhuman experiments that she believes she helped cause, her life dragged deep into despair in the process. There's never a dull moment in Academy City, but no one ever said all of them would be pleasant. [Written by MAL Rewrite]

Long ago, all humans lived beneath the sea. However, some people preferred the surface and abandoned living underwater permanently. As a consequence, they were stripped of their god-given protection called "Ena" which allowed them to breathe underwater. Over time, the rift between the denizens of the sea and of the surface widened, although contact between the two peoples still existed. Nagi no Asu kara follows the story of Hikari Sakishima and Manaka Mukaido, along with their childhood friends Chisaki Hiradaira and Kaname Isaki, who are forced to leave the sea and attend a school on the surface. There, the group also meets Tsumugu Kihara, a fellow student and fisherman who loves the sea. Hikari and his friends' lives are bound to change as they have to deal with the deep-seated hatred and discrimination between the people of sea and of the surface, the storms in their personal lives, as well as an impending tempest which may spell doom for all who dwell on the surface.

The story follows the school life of the three girls, Yuzuko, Yukari, and Yui, who join their high school's Data Processing Club. The odd friendship between the three make for wacky humor in even the most mundane of events.

Rokurou "Rock" Okajima has joined the Lagoon Company, a pirate mercenary group which operates out of Roanapur, Thailand. Despite his initial protests, this filthy slum of depraved souls and merciless criminals now serves as the former salaryman's home. Stranded, with nothing left of his past life but the clothes on his back and his inner morality, Rock is forced to perform jobs alongside the other members of the Lagoon crew. Berated for his lack of spine as he wades through the underbelly of society, he must decide whether to continue on amidst the gunfire and ruthlessness or risk everything he has in an attempt to be free. Whether he chooses the comfort of a familiar land or the freedom of being an outlaw, his decision will have lasting consequences on the crew who gave him a home.