Haruka Nanase's new stage is Sydney, the place of his dreams that he once visited. One day while taking a short break before his departure, Haru has a chance confrontation with a fellow athlete from the All-Japan Invitational. Carrying all the feelings from those he's swam with in his heart, Haru takes his first step forward into a new world. Waiting for him there is the unmistakable champion, Albert Volandel. In the lead up to the Sydney tournament, all the competitors attempt to boost their morale. What is each competitor feeling, and what do they swim for, as they attempt to compete at the top of the world? Their passionate struggle against the water begins from here――！ (Source: Free! website, Translated)

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.

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.

After his first appearance on the competitive world stage, Haruka is held captive by the swimming of the unmistakable champion, Albert, and feels like he's lost his way. With the current state of things, his swimming and what the water means to him are called into question. Haruka begins to sink to the bottom of the murky water as he struggles on his own. Pushed on by a restless urge in his heart, Haruka purposefully puts himself through a rigorous and intensive training regiment, relentlessly devoting himself to practice. In his heart, Haruka knows that he's pushing himself beyond his limits both physically and mentally. His friends can do nothing but watch over and have faith in him. Memories of Albert's cold, dry swimming keep replaying in his mind. I have to get faster, I have to become stronger. I have to compete against Albert again. Haruka unleashes his stroke to cut through the heavy, indifferent water. His friends draw closer to watch. What scenery will Haruka see at the end of this struggle＊──! (Source: Free! website, Translated)