Rin is dispatched as part of the reinforcement unit to the Kyoto field office, which guards the hiding place of the Right Eye of the Impure King. The Myoda sect, led by Bon’s father and responsible for the eye’s defense, has endured the recent attack.

Now that she's re-learned how to ride a bike, Hiromi and Tomoe decide to go on a cycling tour of the city of Kamakura. They go sightseeing with Mori Shiki-sensei, who they run into on their tour, and Hiromi gets lost while practicing during a break.

It’s been two years since the end of the Fourth Great Ninja War. Shikamaru now has an important role within the Hidden Leaf government, and as a representative of the Leaf in the Alliance. One day, a situation develops with shinobi disappearing in droves, and Shikamaru takes on a dangerous mission.

Conan suddenly wakes up in the darkness. While walking with the Detective Boys to go shopping, Conan witnessed a figure breaking open a safe inside a building. Conan was attacked by the culprit and imprisoned inside a rectangular box. Meanwhile, Kogoro is hired to find the thief who stole the will of Karabashi Group chairman Karabashi Gotaro. The suspects have been narrowed down to Kozo the eldest son, Mitsuyo the eldest daughter, and Hideo the second son. Conan manages to get in touch with the Detective Boys using his badge, but he soons finds himself cornered in a desperate situation...