The war on terror exploded, literally, the day Sarajevo was destroyed by a homemade nuclear device. The leading democracies transformed into total surveillance states, and the developing world has drowned under a wave of genocides. The mysterious American John Paul seems to be behind the collapse of the world system, and it's up to intelligence agent Clavis Shepherd to track John Paul across the wreckage of civilizations and to find the true heart of darkness—a genocidal organ.

The story begins the day before the graduation ceremony. Five middle school girls each are preoccupied with their real everyday lives. These girls meet each other in a fantasy world after being sent there through a sudden occurrence. There, they learn about the impending crisis that this world is facing. The way to avert this crisis is for the five to collaborate and bring their five hearts together as one through dance. However, the five cannot come to love the world, and cannot tell their true feelings to one another, so their hearts are unable to unite. The time limit is fast approaching. Can the dance of the five girls save the world? And will they be able to graduate?

After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

A nameless sword wakes up to discover he has been reincarnated from his former life as a human. With his power of telekinesis, he moves around this new world, acquiring several skills and abilities. When the sword comes upon a forest filled with monsters, he meets a young girl fleeing from a beast. Grabbing the sword, the girl easily defeats the monster. After introducing herself as Fran, she names the sword "Shishou" and officially becomes his wielder. The two set out to become adventurers, but unfortunately for Fran, she is a member of the Black Cat Tribe—a Beastkin group with a bad reputation. No member of this tribe has ever evolved into a mightier beast, but Fran plans to be the first and achieve her parents' dream. As Shishou promises to remain her sword until she attains her goal, they form an unstoppable partnership of impressive strength.