In their last year of middle school, the five band members of CRYCHIC went their separate ways after an unpleasant disbandment. Each wrestling with their own regrets, the girls enrolled in different high schools, hoping never to hear from one another again. Meanwhile, Anon Chihaya transfers to Haneoka Girls' Academy in the middle of the school year. As most students play in a band as a hobby, Anon desires to fit in and spends her first days trying to recruit members for her own band, envisioning herself as the group's vocalist. She befriends Tomori Takamatsu, a shy girl who seems interested but hesitant about joining. As it turns out, Tomori used to be part of CRYCHIC, an experience that has scarred her deeply. Through Tomori, Anon meets Taki Shiina and Soyo Nagasaki, both former members of the same band. Although Taki detests the idea of playing with Anon, Soyo is delighted to help her out. Now with Soyo by her side, Anon's dream of forming a band is within reach—if only she could find a few more members.

The Armed Detective Agency is still on the run from the Hunting Dogs, but not all hope is lost. Detective Ranpo Edogawa has a plan to prove the Agency's innocence and save the world from chaos: to find and capture Kamui—the leader of the terrorist organization Decay of the Angel. In order to determine Kamui's whereabouts, Ranpo and his colleague Atsushi Nakajima must convince Genichirou Fukuchi, the renowned captain of the Hunting Dogs, for amnesty. Although Fukuchi was tasked with arresting the members of the Agency, his past with the Agency's president, Yukichi Fukuzawa, may be the key to earning his trust. But unbeknownst to them, Fukuchi might not be as honorable as he proclaims.

The year is 2006, and the halls of Tokyo Prefectural Jujutsu High School echo with the endless bickering and intense debate between two inseparable best friends. Exuding unshakeable confidence, Satoru Gojou and Suguru Getou believe there is no challenge too great for young and powerful Special Grade sorcerers such as themselves. They are tasked with safely delivering a sensible girl named Riko Amanai to the entity whose existence is the very essence of the jujutsu world. However, the mission plunges them into an exhausting swirl of moral conflict that threatens to destroy the already feeble amity between sorcerers and ordinary humans. Twelve years later, students and sorcerers are the frontline defense against the rising number of high-level curses born from humans' negative emotions. As the entities grow in power, their self-awareness and ambition increase too. The curses unite for the common goal of eradicating humans and creating a world of only cursed energy users, led by a dangerous, ancient cursed spirit. To dispose of their greatest obstacle—the strongest sorcerer, Gojou—they orchestrate an attack at Shibuya Station on Halloween. Dividing into teams, the sorcerers enter the fight prepared to risk everything to protect the innocent and their own kind.

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.