Makoto was born in Kazune city, but was forced to move away with his sister Hinata and Minamo’s family after his father’s death. As children, the three played together. When his family moves for the second time, he entrusted to Minamo a harmonica. The two pinky-swore to meet again and marry some day.

The game begins four years later. Makoto and Hinata are returning to Kazune via train and enroll at High School where he is reunited with Minamo. He learns that many people of the city have special powers which only they can do. For example, Hinata can jump higher than most 2-story buildings, Minamo can control the wind, Nozomi can create shockwaves with edged weapons, and Wakaba can cure wounds and slow down diseases. The town is also home to a long series of murders and mysterious disappearances.

When Minamo’s father Professor Akihito tries to research the city’s mysteries to understand what caused these powers to develop, a chain of events begins and in the game it is the player’s goal to help Makoto uncover these mysteries while forging bonds with one of the five girls.