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 limited-edition of the 26th manga volume will include an anime adaptation of the popular special flashback chapter "Uchi ga Kita Machi" (The Town Where I Arrived). The story reveals how Haruto, Akari, and Takashi first met during childhood, and serves as a prologue to the TV anime. The 27th limited-edition manga volume will include a special anime episode produced in full cooperation with Seo Kouji. This OVA will be the animation of the end of the manga. (Volume 27 is the final volume of the long-running series.)

Eba Yuzuki has mysteriously decided to go to high school in the countryside. But despite Kirishima Haruto's objections, she is living in his home. Now he has to put up with a freeloading city girl and even worse, make sure Kanzaki Nanami, the girl he likes, doesn't get the wrong idea!

Disillusioned with the afterlife, a new student causes a scene during a classroom test and expresses his doubts about whether getting good grades can really lead to escaping the school and ascending to Heaven. Afterwards, he is confronted by the new student council president—a familiar face whose past experiences give him powerful insight into the true nature of the school and first-hand knowledge regarding the futility of rebellion. [Written by MAL Rewrite]