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Second year high school student, Haruka Nanase, has a fascination and love for water. He struggles to move forward in life while remembering his elementary school days as a competitive swimmer.
In the present, Makoto Tachibana, Haruka's best friend, goes to pick him up for their second day of school at Iwatobi High. While having lunch that day, they encounter their old friend, and recent transfer, Nagisa Hazuki. Nagisa then suggests that they go to their old dilapidated Swimming Club and dig up a time capsule containing a relay trophy they had won with their friend Rin Matsuoka.
While there, Haruka once again reminisces over a photo of the race, being the last time the group had swam together before Rin had moved to Australia to enroll in a swimming school. Afterwards, the group shockingly runs into a completely changed Rin in the hallways. Rin immediately challenges Haruka to a race, until they discover that the old pool is empty.
The next night, Makoto, Nagisa, and a scarlet-haired girl, afterwards introduced as Gou Matsuoka, Rin's younger sister, pay Haruka a visit. Afterwards, Makoto and Nagisa convince a reluctant Haruka to visit Samezuka by tempting him to a swim duel in the school's pool. Upon arriving, they wait until the school's swimming team is done with practice and break into the academy's swimming pool. They are then discovered by Rin who aggressively orders them out. Haruka then steps out of the pool and challenges Rin to a freestyle match.
After the match, Haruka and the others are once again reprimanded for trespassing on Samezuka Academy grounds.
While continuing the restoration of Iwatobi's outdoor pool, Gou, who was still confused about Rin's behavior, asks Makoto about their race and learns that Haruka threw the match. This allowed Rin to win since he was merely content with being in the water, something which angered Rin.
Later that night Makoto runs into their old coach Goro Sasabe. Sasabe reveals that Haruka and Rin had a race when the latter made a rare return to Japan, of which Haruka easily won. Rin was exceptionally disappointed that his hard work was for nothing, creating a rift between them, subsequently causing Haruka to quit competitive swimming because he had hurt Rin's pride.
When Haruka, Makoto, Nagisa and Gou finally finished the restoration of the pool, Haruka couldn't help but jump in it and swim, much to his friends' dismay.
Haruka catches a cold from his swim in the newly restored Iwatobi High swimming pool. He, Makoto and Nagisa try to find a fourth member for Iwatobi Swim Club and at the end, Nagisa succeeds to get Rei to join them.
At the store where Iwatobi Swim Club is buying new swimsuits, Haruka and Rin run into each other and have a short discussion about their differing forms with Rin wanting a race with them both in peak condition, or else he may no be able to move forward from his loss and both decide to settle the score at the upcoming tournament.
Afterwards, Haruka takes a turn trying to teach Rei freestyle swimming and fails, greatly disappointing Rei. As the day draws to a close, Haruka laments to Rei that he too isn't compatible with other techniques in that he doesn't swim freestyle by choice; merely because it is all he can swim. The next day, having come to this realization, Rei tries the last technique and finds it compatible with himself: the butterfly stroke.
Gou excitedly proposes that they use a decades old training regiment and venture to an island for a summer training camp. They all agree and decide to find sponsors. Later, Haruka expresses concern for Makoto since he had a rather scarring experience with the ocean in the past, to which Makoto reassures that he is fine. This leads to a backstory on Makoto's childhood, as he has always been afraid of the ocean.