Kaito, a puzzle-loving high school freshman, is selected as a candidate for "Phi Brain". He and his friend Nonoha find an "unsolvable puzzle" near their school. The puzzle turns out to be a life-threatening "philosopher's puzzle" created by the mysterious group P.O.G. (Puzzle Of God). After successfully solving the puzzle, Kaito is designated as a Solver and is joined by other Solvers as they battle P.O.G. all over the world by solving the "philosopher's puzzles".