Continuation of Soukyuu no Fafner: Dead Aggressor - Exodus.

2150 AD. The battle against the silicon-based Festums from outer space reaches a new phase. Fragments of the North Pole Mir were scattered throughout the world. Eventually, they began to act on their own as independent Mirs. Most hated humanity and attacked them, but some chose to coexist with mankind. Some with the same way of thinking existed within the human race, as well: those who were both human and Festum. They added to the chaos of the battle and brought about even more hatred.

During Japan's feudal era, there was a war between two ninja clans: the Byakuro and the Kabusu. One night, the Kabusu staged a fierce attack on the Byakuro castle in hopes of kidnapping the clan's infant princess. Their mission was foiled when a loyal ninja of the Byakuro flees the attack with the princess and disappears, eventually raising her to be a ninja. Several years later, six ninja trainees are given a mission to infiltrate the Kabusu-occupied Byakuro castle and retrieve a sacred scroll to complete their training. But their skills are put to the test when they encounter three members of the Kabusu, who use dark sorcery in an attempt to once again capture the princess - who happens to be one of the trainees.