While having lunch at the second day of high school, Haruka and Makoto encounter their old friend, and recent transfer, Nagisa Hazuki. Nagisa not only wishes to swim with Haruka like they used to, but also suggests that they dig up a time capsule containing a relay trophy they had won with their friend Rin Matsuoka at the dilapidated Swimming Club. While at the old swim club building, the group shockingly runs into a completely changed Rin in the hallways. Rin immediately challenges Haruka to a race, and Nagisa and Makoto try to stop them from jumping in the pool, only to find that the old pool is empty. At school the next day, a scarlet-haired girl observes the group with a friend and remarks of them being old acquaintances before Makoto and Nagisa are reprimanded by a teacher for trespassing at the swimming club. As Makoto and Nagisa visit Haruka that evening, they discover the scarlet-haired girl turns out to be Rin's sister, Gou Matsuoka attempting to pay Haruka a visit. They then learn from her that Rin now attends Samezuka Academy upon his return from Australia.
The group, once again, commits trespass, but this time into Samezuka Academy indoor pool, in order to maybe meet Rin again. To Haruka's joy, Rin appears and they have a match, while Nagisa and Makoto stay on the side and watch. After the match, the group is once again reprimanded for trespassing on Samezuka Academy grounds. Makoto and Nagisa run into Gou and they all agree that Rin's attitude had dramatically changed in the past few years, simultaneously learning that Gou had been the one who sent him to the Iwatobi Swimming Club while Nagisa suggests that they form a school swimming club. After getting Haruka on board, Makoto and Nagisa propose the idea to their homeroom teacher, Miho Amakata, who agrees after Nagisa gives her a little prompt. Finally, the club is accepted by the faculty on the condition that they find one more member, and restore the school's swimming pool themselves. Nagisa begins the task of finding a fourth club member, which proves much more demanding than they had initially thought.
While taking the train to school, Nagisa tries to recruit Rei Ryugazaki to join the swim club to which he bluntly refuses. Gou proposes that the swim club join an indoor gym so they can practice swimming until summer, but due to its expense, they seek sponsorship from the school. Miho reveals that they won't get sponsored until their club earns accomplishments in tournaments, but would still require a fourth swimmer. Nagisa informs Haruka and everyone of Rei's perfect candidacy due to his feminine given name. This prompts Nagisa to wait for Rei after practice, much to his surprise and continues to pester him about joining. The next evening, while doing pole vault training, Rei's coach admits that his form wouldn't improve unless he stops calculating his movements beforehand, much to his frustration. Gou informs the club that she had successfully scheduled a joint swimming practice with the Samezuka team at their indoor pool, but they would still require a fourth swimmer. The following morning, Nagisa meets up with Rei on his run to school and explains his reasoning for wanting Rei to join prompting Rei agree on a trial basis.
At the joint Samezuka-Iwatobi practice, Rei tries to avoid swimming in the time trials, but is forced to and much to everyone's surprise, it is revealed that he cannot swim. The next day at his pole vaulting practice, Rei doesn't use his calculations and falls. He approaches the spectating Nagisa and everyone and admits that he would like to achieve a form similar to Haruka's and officially joins the swim club while tasking Nagisa with teaching him how to swim.
The Swim Club officially starts training in the refurbished pool using an old training regiment of Gou has had unearthed. Rei's inherent academic skills at learning all the swimming theory prove to be useless since his body refuses to move in the water. Nagisa and Makoto start teaching Rei how to swim and learn that while he can float, his problem still eludes them. The following day, the guys try to come up with designs for a club uniform but Gou instead gives Rei's lessons higher priority and makes a revamped swimming regiment during which he must master swimming in one week before their first prefectural tournament. Nagisa and Makoto try and fail to teach Rei their signature techniques; the breaststroke and backstroke respectively causing Rei to blame his inability on their teaching methods.
Believing that the added pressure will help the Swim Club in their training, Gou continues to make her countdown calender for the upcoming prefectural tournament. Meanwhile, as the guys decide on which events they will each participate in at the tournament, Gou discovers a decades old training regiment of the past Iwatobi Swim Club, and excitedly proposes that they use it and venture to an island for a summer training camp. On the day of the trip, Goro 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. The commotion wakes up Haruka and Nagisa, who follow. Nagisa rescues Rei and Haruka brings Makoto, who has been strangely affected by the ocean, to safety. Rei apologises to Nagisa for making all of them worry and tells him that he saw Makoto come to rescue him, but he didn't look like his usual self. Nagisa and Rei go to find Makoto and Haruka at the other side of the island. The group decides to look for a shelter where they can stay until the storm stops and finds Sukishima Rest House nearby. As they enter the rest house, they find a kitchen and start looking for some food, since all of them are starving. As they're eating around the table, they started talking about their current situation. Haruka then suggests that they spend a night there since there were no signs that the rain was going to stop soon. Nagisa then gets the idea for them to play a game while they're staying in the rest house. All of them got to say something about their past or to do something (Rei had to tell an embarrassing story, Haruka had to tell a love story and Nagisa imitated rockhopper penguin). They later go outside to see a beautiful sky above them, as the rain has stopped. As Rei tells the group about the constellations he sees in the sky, Nagisa notices a puddle beneath them that reflects the beautiful starry sky. Makoto looks at his friends and smiles.
The next morning, the group swims back to the coast where their tens are, as well as Gou and Miho, who didn't know what happened last night. Rin sees them while jogging and wonders what they're doing. When they finally arrive at the coast, Gou and Miho watch them as they sleep and wonder what they're doing. Gou tries to wake them up, but doesn't succeed.
Gou and Makoto watch as Haruka and Nagisa swim. Gou is amazed by Haruka's timing and tells him that it's his new personal record. Everybody agrees that their training camp has paid off. Gou then tells Nagisa that he'll have to train a little more, but then Makoto tells her that they all have come so far in such a short time. While the guys are eating their lunch, Gou finds them and shows them the pictures that she took during their summer camp. While the rest looks over the pictures, the one that has captured Haruka's attention is a picture of Rin. Nagisa whispers to Makoto that racing with Rin motivates Haruka.
At the tournament, Haruka looses to Rin and the next race starts. Goro finally finds the group watching races and apologises for being late. Nagisa gets angry with him for showing up late, but Miho interferes thanking Goro for helping them the other day. Goro says once again that he thinks that he knows her from somewhere, but Miho denies and turns away from him. After Nagisa scolds Goro for trying to hit on Miho (which Goro immediately denies), Rei tells him that Haruka had already swam him freestyle heat. As Makoto prepares himself for his race, Goro asks Nagisa and Rei where Haruka is, but Rei tells him that they couldn't find him. Nagisa runs away telling them that he is going to find Haruka because he wants him to watch them swim. He finds Haruka sitting in the hallway wondering if things would be different if Rin won the race they had before he went abroad. He tells Haruka that Makoto's race is about to start and that he should go and watch him swim. Haruka then tells him that he'll pass, but Nagisa grabs his hand and runs with him to the pool.
Nagisa is up next for a race. When his race starts, Goro, Miho, Gou, Rei and Makoto cheer for him, like they did for Makoto as well, and Haruka still stands speechless as he watches Nagisa swim. Nagisa comes back to where others are with a defeated look on his face. He apologizes for not making it and Goro and Gou comfort him. As soon as the first day of the tournament ended, Miho and Goro left Makoto, Nagisa, Rei and Gou alone. Gou then decides to tell the group that she signed all of them up for the medley relay on the second day of the tournament. The group protests a little for Gou not telling them about it sooner, but Rei immediately agrees on swimming in the relay, making Makoto and Nagisa agree as well. They go to Haruka's house with the goal to make him agree on swimming in the relay with them as well, but nobody's there. They break in the house and start searching for Haruka in the hope that he's somewhere in the house. After going in every room and not finding him there, they decide to call him, but he doesn't answer. After Rei, Nagisa and Gou leave him a voice message, they spot his phone in the house. Makoto then tells them that Haruka doesn't bring his phone with him often.
Next morning, the phone's ringing wakes Nagisa up. Ha answers the call and finds out that Haruka will swim in the relay with the rest of them. Just when Gou mentions that Nagisa and Rei are still missing at their meeting spot, they appear running towards them, apologising for being late. Nagisa reveals to them that they were at Iwatobi High's outdoor pool practising for the relay, and that there's no possibility of Rei completely failing. The group decides to give it their best shot and enters the venue.
Nagisa and Makoto are at Haruka's house, persuading him to go the the festival. Makoto says that there is a shrine for the god of water, and Nagisa adds that Rei is waiting for them, and that he says that the four of them must attend together or else it would be meaningless. Haruka agrees to go, surprising Nagisa and Makoto. While deciding what food they want, Rei spots Rin and Aiichiro and nudges Nagisa, bringing it to his attention. Nagisa successfully blocks Haruka from spotting Rei, and says that he will go and buy burgers for everyone, wanting Haruka to wait at a rest area. Makoto gets the hint from Nagisa's winking and leads Haruka away. Nagisa tells Rei that he invited Haruka to the festival to get his mind off swimming but now it might have the opposite effect. They speculates that the worst case scenario would be to have Haruka quitting the relay. Nagisa comes up with a plan, asking Rei to follow Rin and update him on his whereabouts so that Nagisa can lead the others away.
On the way home from school, Nagisa asks Rei what is wrong and Rei replies that he does not understand why Rin suddenly decide to take part in the relay. He complains that their goal is to make it to the national as a team but everyone is talking about Rin instead. The team, along with Gou and Miho are over at Goro's house, eating hot pot even though it is in the middle of summer. When Nagisa accidentally upsets a stack of old magazines, Goro realises that the reason he found Miho familar was because he saw Miho being a model for swimsuits in his magazines.
The night before the regionals, Haruka meets Nagisa, who tells him that he is out looking for Rei since he is not in his room. At a playground, Nagisa tells Haruka that he is nervous about tomorrow, surprising him. Nagisa explains that he is scared of screwing up tomorrow, and ruining the relay for everyone. However, Haruka tells Nagisa that it is all thanks to him that they are racing Rin tomorrow since he came up with the idea of creating a swim club. Nagisa agrees and jokingly tells Haruka that he should show more gratitude to him. When Haruka agrees and thanks him, Nagisa is taken aback before being overjoyed and jumps on him.
As Rin miserably fails at his race at the regionals, the team decides to go and search for him. They are running out of time, as the relay is starting soon, but the team makes it just on time. When it is Rei turn to swim, Gou, Goro and Miho stare in shock while Aiichiro and Seijuro also spots Rin. Iwatobi High achieves the first place and Nagisa starts crying tears of joy. Outside the building, Miho is telling them off for pulling off such a stunt. They were disqualified and had to endure a scolding from the staff there. When Goro asks the reason for their actions, Rei says that it is only right and the rest agrees, saying that even though they are from different teams, they are still teammates.