Approximatly 20 years ago, a slave boy named Yuto manages to escape from Mariejois, where he had been used and experimented by the world nobles. At the same time, a girl named Kay, who is of significance for the World Government, suddenly disappears. Years later, Yuto creates a pirate crew whose goal is to stop the World Government from enslaving people. The paths between the boy and the girl cross and together they strive to free others from similar misery. However, they soon realise that the World Government have other plans.