When a tragedy befalls their fellow students on graduation day, three pupils of the Hayate Way's Ninja Academy must take on the Jakanja — a clan of evil space warriors. But they can't do it alone. Can they find the help they need? And can the young warriors act swiftly enough to defeat the Jakanja before they destroy the known universe?

Just a few years prior, automata served as weapons in the great war. Now that the war has ended, these machines with human hearts search for their place in an unfamiliar, peaceful world — and their search begins at the Kuronekotei café.