Set between the events of Free!: Eternal Summer and Free!: Dive to the Future, Free!: Take Your Marks depicts the graduating seniors' final summer through four distinct stories before they embark on their future journeys. Unmei no Choice! (Destined Choice!) follows Haruka Nanase and Makoto Tachibana as they search for a new apartment for Haruka while he settles into Tokyo. Hitou no Cooling Down! (Cooling Down at the Secret Hot Spring!) features Aiichiro Nitori selecting a graduation gift for Rin Matsuoka and Sousuke Yamazaki, while Momotaro Mikoshiba wins tickets to the Anago Hot Springs. Hoping for a shared trip, Aiichiro and Momotaro invite Rin and Sousuke. Kessoku no Batafurai! (United Butterfly!) shows Rei Ryugazaki, Nagisa Hazuki, and Gou Matsuoka producing a recruitment video to attract new club members for the upcoming school year. Tabidachi no Etanaru Buru! (Departing Eternal Blue!) explores the Iwatobi and Samezuka swim teams' plans for Rin's surprise farewell party, as he is set to depart for Australia soon.