Misuzu Moritani is an introvert who has always had difficulty interacting with her classmates, quickly becoming flustered whenever someone tries to talk to her. Sometimes, she will use her ability to stop time for three minutes to escape troublesome social situations. One day, as Misuzu watches the suspended environment around her, she observes that her classmate, Haruka Murakami, is somehow able to move despite her temporal influence. From that moment on, Misuzu experiences new wonders as she explores more of the world she has long avoided; no matter where time may take her, Misuzu can count on Haruka to always be at her side.

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.

Hundreds of years ago, the Chinese zodiac spirits and their god swore to stay together eternally. United by this promise, the possessed members of the Souma family shall always return to each other under any circumstances. Yet, when these bonds shackle them from freedom, it becomes an undesirable burden—a curse. As head of the clan, Akito is convinced that he shares a special connection with the other Soumas. While he desperately clings to this fantasy, the rest of the family remains isolated and suppressed by the fear of punishment. Tooru Honda, who has grown attached to the Soumas, is determined to break the chains that bind them. Her companionship with the family and her friends encourages her to move forward with lifting the curse. However, due to confounding revelations, she struggles to find the tenacity to continue her endeavors. With time slowly withering away, Tooru contends with an uncertain future in hopes of reaching the tranquility that may lie beyond all this commotion.

Recap of the Free!: Dive to the Future TV series featuring new scenes.