Some time ago, Jin Makata lost his memories when battling against Count Pythagoreas. Now that the Orpheus Order has been defeated, Kaito, Nonoha and Rook are determined to restore the man to his former self by bringing him to familiar locations, and soon arrive at the Fool’s Puzzle from their past. But things escalate when a mysterious girl named Raetsel ambushes them in the puzzle’s chambers; she works for an organization called Master Brain, and she’s come to steal Jin away. And not only does Jin recognize the girl, but she also claims that Master Brain’s goal is to rid the world of puzzlers at Jin’s request! Now, it’s up to the Children of Phi Brain to discover the truth and put a stop to the organization’s nefarious plans.