Rei Ryugazaki was initially in the school's track team, but is constantly pestered by his classmate Nagisa to become the vital fourth member of their newly-founded swim club after Nagisa found out that Rei had a feminine name and believed it to be fate (since the other swim club members have feminine names, too). After realizing not all activities are based off calculations and seeing Haruka swimming beautifully, he eventually accepts the offer.
While training for the upcoming tournament, the Iwatobi Swim Club sees that Rei was able to float in water and his form was perfect. Though said, he can't move while performing the needed actions for different strokes, and constantly sinks to the bottom of the pool when trying. Gou gives him a week to learn how to swim, with every member teaching him their specific strokes, but always failing. It wasn't until Rei sits with Haruka and talks about just diving in freely did he find out that the butterfly stroke was the one he could perfect, since it was the only stroke he still didn't try.
On the day of the trip to the summer training camp, Sasabe takes the Swim Club to the island where they coincidentally discover the Samezuka Swim Club, along with Rin, training at a special swimming facility on the island. After the guys get settled on the beach they begin their stamina training regiment which involves making three long-distance swimming circuits between the deserted islands of Sukishima, Oshima, and Mizushima. At the end of the first day, the club only manages swimming half of their goal, leaving Rei to feel a bit disappointed for lagging behind.
That night, unable to sleep due to his performance, Rei heads into the ocean to continue training when a sudden storm takes him by surprise. Makoto awakens at that moment and goes looking for Rei, frantically diving to his aid upon hearing Rei's cries for help.
Rei is struggling to stay afloat against the strong current while Makoto tries to save him. After the ordeal, Nagisa and Rei rest at a nearby island where Haruka and Makoto are at the other end of the island. They begin to search and eventually seek a shelter overnight at Sukishima Rest House, an abandoned and creepy looking building where Rei shares his embarrassing moment during a field trip in fifth grade. When day break, they race each other back to their campsite where Gou and Miho are and sleep at the beach after a long and tiring night.
After the gang prayed at a local shrine, Rei expresses interest in participating in the relay in the tournament as he had rented a video of the Olympics where he found that swimming in a relay can be beautiful as four swimmers swim in different styles in succession to complete a race together. On the day of the tournament itself, Rei gets too nervous at the atmosphere at the tournament venue and Nagisa tries to encourage Rei telling him to relax and ultimately have fun.
Rei, Makoto and Nagisa go to search for Haruka but Rin was not much of a help for them. Makoto suggests that they leave Haruka alone and let him cool down, after all, their individual events are coming up soon. Like the rest of the team, Rei didn't manage to get into the finals. As the tournament comes to an end, they realize that Haruka has gone without them. Gou then tells them that she had secretly signed them up for the relay segment and Rei agrees that they should try their best at it as it was their last and final chance if they want to get into the finals.
The team manages to win the relay segment and is able to proceed to the regional. During the morning assembly, the school Principal announces that Iwatobi Swim Team had secured a place in the regional and wishes them all the best in hope that they could advance to the finals. The team goes to the Summer Festival later at night where they visit the shrine to pray before their regionals. Rei and Nagisa happen to see Rin at the festival too, thus Rei gets tasked to follow Rin so that Nagisa could avoid them meeting at the festival.
After the team finishes on one of their practices, Nagisa, Makoto, Rei and Haruka together with Gou, Goro and Miho have a hot pot in Goro's house even though it's summer. On the way home, Rei asks the other three (Nagisa, Haruka and Makoto) on what happened to their relationship with Rin, knowing that the old photos showed how close they were before. Haru tells Rei about Rin's obsession on swimming relay and that event where Rin and Haru raced which ended Rin's loss when he came back from Australia. The next day, Rei skips practice and goes to Samezuka Academy to talk with Rin.
Rei asks Rin about why he is participating in the relay, what changed him after he left for Australia and what he actually wants from Nagisa, stating his desire to be a part of their team. Later, Haruka and the others come over to Rei's place, where they assure Rei he is an irreplaceable team member. After arriving at the location for the regional tournament and checking into their hotel, the group go to see the pool they'll be swimming in. Later that night, as everyone is too excited to sleep, Rin asks Rei to meet up with him, explaining that the reason he quit swimming was because he struggled to swim the way he used to and felt he couldn't reach Olympic level. Before taking his leave, Rin tells Rei that he needs to make sure he doesn't embarrass Iwatobi's team when they compete against each other.
After Rin runs off in an outburst, telling Aiichiro that he will quit swimming, Haruka and the others overhear Rin say he was taken out of the relay, which comes as a shock to Haruka. It is at this point that Rei tells everyone about what Rin told him the previous night, stating his belief that what Rin wanted wasn't to win, but to swim with everyone again. With the relay preliminaries approaching fast, the gang splits up in search of Rin, who is eventually found by Haruka. Making it just in time for the preliminaries, Rei lets Rin take his place in the relay, allowing him to finally swim with his friends. Although the Iwatobi team is inevitably disqualified for their unapproved roster change despite placing first, they feel proud in doing what they thought was the right thing.