Shinya Kougami continues to wander the Southeast Asian Union (SEAUn) away from the eyes of the Sibyl System in Japan. While travelling through the Tibet-Himalayan Alliance Kingdom, Kougami encounters Guillermo Garcia—commander of a paramilitary group attempting to unite the local factions and bring peace to the war-torn nation. Wary of joining another mercenary group, Kougami declines to join his cause, but agrees to be driven to the nearby Tibetan capital by one of Garcia’s men. However, Kougami's plan to remain uninvolved is short-lived when a bus of refugees are ambushed by armed guerrillas. Among them is a half-Japanese, half-Tibetan girl named Tenzing Wangchuck. Impressed with Kougami's fighting prowess as he single-handedly takes the attackers out, Wangchuck requests him to teach her how to fight so she can take revenge against the warlord who murdered her family. Knowing first-hand that there's no turning back to the person you were once you take a human life, Kougami is initially reluctant to accept her request. But faced with the girl's desire for vengeance that mirrors the haunting abyss inside his own heart, will he train her?

Due to the incredible success of the Sibyl System, Japan has begun exporting the technology to other countries with the hope that it will one day be used all around the world. In order to test its effectiveness in a foreign location, the war-torn state of the South East Asian Union (SEAUn) decides to implement the system, hoping to bring peace and stability to the town of Shambala Float and keep the population in check.

However, a group of anti-Sibyl terrorists arrive in Japan, and the Ministry of Welfare's Public Safety Bureau discovers significant evidence that the invaders are being aided by Shinya Kougami, a former Enforcer who went rogue. Because of their past relationship, Akane Tsunemori is sent to SEAUn to bring him back, but with their last meeting years in the past, their reunion might not go quite as planned.

Taking place between the events of Free!: Eternal Summer and Free!: Dive to the Future, Free!: Take Your Marks plays out the graduated seniors' last summer through four different stories before they set sail for the future. Unmei no Choice! (Destined Choice!) follows Haruka Nanase and Makoto Tachibana searching for a new apartment for Haruka as he settles into Tokyo. Hitou no Cooling Down! (Cooling Down at the Secret Hot Spring!) sees Aiichiro Nitori choose a graduation gift for Rin Matsuoka and Sousuke Yamazaki, while Momotaro Mikoshiba wins tickets to the Anago Hot Springs. Hoping for a trip together, Aiichiro and Momotaro invite Rin and Sousuke. Kessoku no Batafurai! (United Butterfly!) shows Rei Ryugazaki, Nagisa Hazuki, and Gou Matsuoka creating a recruitment video to attract new club members for the next school year. Tabidachi no Etanaru Buru! (Departing Eternal Blue!) looks into the Iwatobi and Samezuka swim teams' plans for Rin's surprise going-away party, as he will be departing for Australia soon. [Written by MAL Rewrite]

In Touto Stadium, a J. League soccer match is taking place. During this, Detective Kogorou Mouri receives a bomb threat from an unknown caller and a mysterious riddle that points to its location. Conan Edogawa must now save the fans of the game before the time runs out.

Fortunately, with Conan's quick actions and clever thinking, the bomb is discovered and the explosion is evaded. The culprit does not stop there; Detective Kogorou is informed of another hidden bomb set to explode at a large event in the city. Forced into a race against time, with thousands of more lives at stake, Conan must decipher another riddle, discover the place of the bomb, and catch the culprit in order to escape a terrible tragedy.

[Written by MAL Rewrite]