The anime takes place in 2006, and centers on Akio Hoshigami, who due to a leg injury is forced to give up on her dream of being a track-and-field star. Akio and her friend Ayano Umisoe move on to high school together. Amidst new activities and meeting new friends, Akio gradually starts acting like herself again. Then one day Ayano suddenly disappears.

The movie will focus on Ai Haibara's past and will reconstruct the Mystery Train arc from the television anime, which shows Haibara and Conan meeting for the first time. The movie will also include scenes from the Kurogane no Submarine (Black Iron Submarine) movie.

Movie adaptation of Tsurune: Kazemai Koukou Kyuudoubu.