Between Free!: Eternal Summer and Free!: Dive to the Future, Free!: Take Your Marks delves into the final summer of the graduated seniors through four distinct narratives before they embark on their future journeys. In 'Destined Choice!', Haruka Nanase and Makoto Tachibana navigate the search for a new apartment in Tokyo as Haruka settles into the city. 'Cooling Down at the Secret Hot Spring!' follows Aiichiro Nitori picking a graduation gift for Rin Matsuoka and Sousuke Yamazaki, while Momotaro Mikoshiba wins tickets to the Anago Hot Springs and hopes to share the experience with them. 'United Butterfly!' showcases Rei Ryugazaki, Nagisa Hazuki, and Gou Matsuoka producing a recruitment video to attract new club members for the upcoming school year. Lastly, 'Departing Eternal Blue!' delves into the plans of the Iwatobi and Samezuka swim teams for Rin's farewell party as he prepares to leave for Australia.