Rin Matsuoka’s childhood friend, Sousuke Yamazaki, has recently transferred to Samezuka Academy. Upon their reunion, the two reminisce about their childhood days and reaffirm their wish to swim together. Now with Rin, Sousuke, Captain Mikoshiba’s younger brother Momotarou Mikoshiba, and hard-working Aiichirou Nitori, the Samezuka relay team is formed, and their friendship deepens. However, as tournaments, races, and training go on, the reason for Sousuke’s sudden return begins to trouble him and affect his swimming. Noticing Sousuke’s change, Rin pushes to uncover what is holding him back.

Haruka Nanase has reconciled with his rival Rin Matsuoka, and they have re-established their friendship, determined to race each other again. Now Haruka, along with Makoto Tachibana, Rei Ryuugazaki, and Nagisa Hazuki, prepare for their upcoming tournaments, determined to compete wholeheartedly and achieve victory as a team. At Samezuka Academy, Rin resolves to do the same. Further, the seniors near graduation, and Rin has decided his future plans. However, Haruka and Makoto remain uncertain, and they begin to feel the pressure of having to choose their own paths.

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)

Haruka Nanase has a love for water and a passion for swimming. In elementary school, he competed in and won a relay race with his three friends Rin Matsuoka, Nagisa Hazuki, and Makoto Tachibana. After claiming victory at the tournament, the four friends went their separate ways. Years later, they reunite as high school students; however, Rin couldn't care less about returning to the way things used to be. Not only does he attend a different school, but the sole thing important to him is proving that he is a better swimmer than Haruka. After the bitter reunion, Haruka, Nagisa, and Makoto decide to form the Iwatobi High School Swim Club, but they will need a fourth member if they hope to take part in the upcoming tournament. Enter Rei Ryuugazaki, a former member of the track team whom Nagisa recruits. As the time to compete draws near, the four develop a close bond while training intensely to come out on top and settle things between Haruka and Rin once and for all.