A series of natural disasters has reduced the world to rubble, with the survivors doing whatever they must to survive in a world gone mad. But one young boy, Kakugo, gifted with amazing martial arts and a superpowerful suit of armor by his late father, has been charged with making the world (or at least his school) a safer place. But his sister has a matching set of skills and equipment, and she`s on a mission to bring peace to the world... by wiping out humanity! (Source: AnimeNfo)

Born from the strong emotions of their creators, self-contained pocket dimensions known as Phenomenon have begun forming across Japan. These false worlds overwrite the reality of an affected area and will only be undone if the maker is defeated or appeased. In response, a military-sponsored task force known as Trinary is formed, and its three members—Miyabi Koigasaki, Gabriela Lotaryńska, and Ayami Kunimasa—specialize in dispersing Phenomenon. Caught in one of these Phenomenon during her favorite idol's concert, Tsubame Ouse is saved by the timely arrival of Trinary, and together they are able to resolve the incident. After these events, Tsubame, along with newcomer Kagura Uzuki, decides to join the current Trinary team. As the girls struggle to balance their everyday lives and their responsibility to handle each new Phenomenon that appears, they realize that their own reality also has its own distinct set of problems.

The dawn of a decisive battle nears in Leyte Gulf against the Abyssal Fleet, the mysterious enemies that occupy the sea. As the only ones capable of fighting them, Kanmusu—young girls possessing the souls of warships—reorganize in preparation. The Shiratsuyu-class destroyer Shigure is assigned to the First Striking Force, Third Section—also known as 1YB3H. Unfortunately for Shigure, 1YB3H consists of the remaining few Kanmusu and serves as a diversionary fleet. Needing to confront the Abyssal Fleet head-on, it may well be their first and final mission together. Even so, Shigure refuses to let the enemy take another comrade from her. As they advance toward Leyte Gulf during this suicidal mission, the members of 1YB3H must support each other and persevere to prove their worth as competent ships.

In the year 2063, space travel is feasible and commercially available. As the cheerful Aries Spring arrives at the spaceport to attend a camp on the distant planet McPa, her purse is suddenly snatched by a reckless thief. Luckily, the athletic Kanata Hoshijima is able to retrieve it for her, and Aries soon discovers that he is among the group of teenagers who will be traveling with her on the excursion as team B-5. Upon arriving at their campsite, the group's trip takes a turn for the worse when a strange sphere of black light sucks them into the vast reaches of outer space. Stranded with seemingly no hope, they find an abandoned ship nearby that provides them with the means to return home. However, they soon discover that they are not as close to their campsite as they initially thought, but are in fact thousands of light-years away from home. With this realization, the nine members must cautiously manage their resources, maintain their strength, and unite as one to conquer the darkness of space together. While the reason behind their trip's sudden obstruction remains unknown, they nevertheless embark on the treacherous voyage back home aboard their new ship, the Astra.