Regardless of how students handle the many academic challenges facing them, they all know that there will come a day when they will leave all the hurdles of scholastic achievement behind and tackle the triumphs and sorrows of true adulthood. One thing that many young people don`t realize is that this often means leaving behind the friends that have been with them through their youth.

Marika Katou, a third year student at Hakuho Girls' Academy, is a legitimate space pirate with a Letter of Marque. Between her studies, leading her school's space yacht club, working part time at Cafe Lamp, and being the captain of the space pirate ship Bentenmaru, Marika's days are very busy. One day, Marika gets a job to rob a high-class passenger ship, and she discovers that on the passenger list is Kanata Mugen, a boy who owns a "galaxy pass". Thus, an adventure featuring a hyperspace race between pirates and one young boy begins.

Characters from various games released by Falcom (e.g. Dragon Slayer, The Legend of Heroes, and Ys series) come together in a school.

August 1945. In a converted theological seminary on the outskirts of Nagasaki, a young doctor works to help his patients, as unsettling news comes of a new weapon used by the Americans on the city of Hiroshima. When the second nuclear weapon is dropped on Nagasaki, the hospital staff must work to save lives in the midst of the concentric circles of death that their city has become.