"Free!: Take Your Marks" takes place during the period between "Free!: Eternal Summer" and "Free!: Dive to the Future," centering on the final summer before the graduated seniors start their new journeys. The movie features four individual storylines that delve into each character's future plans. In "Destined Choice!" (Unmei no Choice!), Haruka Nanase and Makoto Tachibana venture to Tokyo to look for an apartment, as Haruka adjusts to his new life. "Cooling Down at the Secret Hot Spring!" (Hitou no Cooling Down!) focuses on Aiichiro Nitori, who is on a quest to find the perfect graduation gift for Rin Matsuoka and Sousuke Yamazaki. Meanwhile, Momotaro Mikoshiba wins tickets to the Anago Hot Springs, and the group hopes to enjoy the trip as a team. Rei Ryugazaki, Nagisa Hazuki, and Gou Matsuoka are the stars of "United Butterfly!" (Kessoku no Batafurai!), as they produce a recruitment video to lure in new members for the swim club's upcoming school year. Finally, "Departing Eternal Blue!" (Tabidachi no Etanaru Buru!) takes a closer look at the farewell party plans of the Iwatobi and Samezuka swim teams, as Rin Matsuoka prepares to depart for Australia.