High school student Azusa jumps off from the rooftop of a school building, but she survives. One month later, the school is taken over by group of people wearing bizarre masks. A pregnant teacher is imprisoned, while the head director of the school and male students disappear. Azusa then finds pieces of a puzzle in an envelope given to her by classmate Shigeo. The puzzle pieces holds the key to solve the case. Azusa chases after Shigeo and she sees something which is unimaginable.

Puzzle is based on Yusuke Yamada's novel by the same name.