As Raetsel challenges Kaito to face her in the Puzzle of God before Jin and Pythagoras, they are greeted by Nonoha who, in this timeline, had grew into a POG Solver. Her feelings that puzzles are solved with the feelings of others break through to Raetsel, bringing her and Kaito back to reality, where they continue the puzzle. Kaito uses his skill to allow Raetsel to win the puzzle, and they are both brought to the top of the tower, where Orpheus attempts to possess Kaito. However, Rook, who had faked his own death, uses Cubic's system to prevent Orpheus from taking over Kaito's mind, whilst Kaito reveals Orpheus and Jin had already merged together. After coming to understand that the thing Kaito had what he and Raetsel lacked was the ability to have fun with puzzles, Jin gives his final wishes to Kaito before passing away. Some time later, as everyone graduates from Root Academy, Nonoha manages to solve the puzzle Jin left behind and heads off in search of Kaito, who is out helping kids enjoy puzzles.
