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While Haruka, Makoto and Nagisa were walking down the corridors of the old Iwatobi Swim Club building, they run into a young man. When they find out that it is actually Rin in front of them, completely changed, they are shocked. He immediately challenges Haruka to a race, until they discover that the old pool is empty.
Haruka, Makoto and Nagisa learn from Rin's sister, Gou Matsuoka, that Rin had returned from Australia and that he's now attending Samezuka Academy. 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.
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. Upon learning this, Makoto calls Rin to inform them of their plans while Rin decides to join the Samezuka swim team for his own grudge against Haruka.
Hoping to bring her brother and his old friends closer, Gou arranges for a joint practice between the Iwatobi and Samezuka swim teams. Upon learning about this, Rin questions what his sister's true intentions really are, but shows no sign of protest. With a new member, Rei Ryugazaki, on their team, the Iwatobi swim club shows up, ready to swim with the first year students of Samezuka. Rin leaves the room, dismissive as he says how their team is nothing but a waste of his time, but shortly after reappears in the bleachers, curious, as Gou notes, about how they will all perform.
Following the joint practice, Rin often spends his free time practicing and training his body, taking along his roommate and fellow swimmer, Aiichirou Nitori. After another night of vigorous training, Aiichirou mentions offhandedly how inspirational watching Haru's team had been, much to Rin's displeasure. As Rin prepares to leave for a jog, he says their team is out of shape and needs to improve immensely before they end up in any tournaments together. Supposedly Rin wants to feel gratification for beating Haru, and he knows he cannot accomplish this if Haru is not even in his best physical condition.
At the store where Iwatobi Swim Club was buying new swimwear, 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 not be able to move forward from his loss and both decide to settle the score at the upcoming tournament.
Upon Iwatobi Swim Club arriving on the island, they coincidentally discover the Samezuka Swim Club, along with Rin, is training at a special swimming facility on the island. As Iwatobi Swim Club prepare for dinner, Gou heads to a nearby convenience store and briefly runs into Rin who shows some concern for Makoto after Gou explains their training, before returning to his usual stoic self. He then offers Gou to walk her to the hotel she's staying in.
Unaware of the trouble the Iwatobi boys are in, Rin wakes up in the middle of the night to the sound of a storm raging just outside his window. Early the next morning, he runs along the beach but pauses when he spots the two tents the Iwatobi team set up for the night. Shortly after seeing them swimming back to shore, however, Rin runs off to continue his practice.
It's the day before prefecturals and Rin wakes up from a harrowing nightmare involving his father. The dream begins with Rin visiting Haru's house. When no one comes by to open the door, he invites himself in and finds a goldfish bowl with a single goldfish swimming about inside. The sound of footsteps distracts him and, startled, he turns to find Haruka standing in the doorway. After the boy tells him he only swims freestyle, Haru walks away but Rin promptly chases after him only to end up at the edge of a large swimming pool. He's about to engage in a race, it seems, but before he can reach his starting platform he spots his father as a child, holding a large trophy he won in a medley relay with his team. His father runs and once again Rin pursues, chasing him from the pool to the narrow streets of Iwatobi. Ultimately he loses sight of him after passing through a bright tunnel and ends up in a procession of old priests in white clothing. Rin runs against the men but pauses to look back, catching sight of a younger version of himself holding his little sister's hand. The child Rin mutters something incoherently just before Rin startles himself awake, shaken, gasping, and sweating with fright.
At practice that day, Aiichirou confronts Rin and asks him why he decided to join the 100 meter freestyle crawl rather than the butterfly, which is Rin's best stroke. Rin dismisses the conversation, though Aiichirou suspects Haru may be involved in Rin's decision. That evening Aiichirou brings up the conversation with Rin again as he helps him train in their room. Aiichirou confesses he's upset with Rin for choosing a freestyle crawl when he clearly has the potential for something much greater. He admits he himself wanted to be in the 100 meter crawl instead to which Rin seems to express a bit of regret. However, Rin boosts Aiichirou's confidence when he tells him he has enough endurance to last in the 400 meter crawl he was assigned to anyway. After telling Aiichirou he will be visiting his father's grave, he goes on to explain the story of his father's past as well as his reasons for wanting to become an Olympic swimmer. Rin says that if he cannot finally beat Haruka in a true race, then he will not be able to move on and accomplish that goal.
On the day of prefecturals, Rin revisits his father's grave, telling him once again to watch out for him as he wins his big race.
Haru and Rin meet for a brief moment in a hall of the facility where prefecturals will be held. Rin tries to rile Haru up by telling him he may not even make it to the finals to race him and ultimately Haru does lose without even placing in the finals. As Rin exits the water, confident and cocky after his first place win, he tells Haru he will no longer swim with him ever again, a statement which hurts Haru and leaves him silent and alone in the pool.
Haru shortly leaves for the locker rooms after his loss, though his long absence leaves his team concerned and they rush into the building to search for him. In doing so they bump into Rin who boasts his win and tells them there is nothing more important to him that winning in a swimming race. Makoto interjects, however, telling Rin that what truly matters in a race is swimming together with one's teammates. Rin abruptly cuts him off then strides away, not wanting to deal with any further confrontations or sentimental speeches with the Iwatobi team. Regardless, as Rin spends his time waiting in the Samezuka bus, he cannot help but think over Makoto words about how Haru wanted to swim with him more than anything.
In the end, no one in the Iwatobi team manages to make the cut for finals, but Gou surprises them all when she confesses she signed them all up for the medley relay portion of the preliminaries tomorrow. That day, as Rin sits by himself in the hall, Aiichirou approaches him, excited when he says the Iwatobi team will be swimming in the relay. Something seems to spark inside of Rin and he promptly runs out to watch. As each swimmer breaks the surface of the water he comments on their unique swimming style he remembers all too well from when they all used to swim together. Watching Rei swim, however, irritates Rin, because Rei has since replaced him, it seems, as their team butterfly swimmer. As Haru jumps in, Rin watches on in anticipation.
Haru eventually wins the race for the team and as they all celebrate together Rin can only watch on in silence, his thoughts drifting to when they all won and swam together as children.
Summer time rolls around and the streets of the Iwatobi Prefecture light up with squid shaped lanterns and rows upon rows of brightly colored stalls during the annual Squid Festival. The Iwatobi boys venture out to enjoy themselves at the event but both Nagisa and Rei end up distracted when they spot Rin and Aiichirou walking together amidst the crowd of people. Wanting to keep Haruka and Rin from meeting in case they break into some sort of confrontation, Nagisa has Rei spy on Rin while keeping in touch with him through text messages. Eventually, however, both Makoto and Haruka discover Rei and Nagisa's plans just as Rei manages to follow Rin all the way out to a small old building on the outskirts of the festival. The building is Iwatobi Elementary and just beyond the chained link fence Rin spots the large cherry blossom tree standing proudly before a small swimming pool. Once again his thoughts drift to memories of when he was a child, laughing, swimming, and having fun with his teammates. Their voices resound in his mind and he remembers how it used to feel to cheer each other on in the heat of a race. Shortly after, Rin breaks into a run back towards the Iwatobi train station where he confronts Captain Mikoshiba to inform him he wishes to participate instead in the medley relay.
After the festival, Rei expresses his confusion about Rin and the Iwatobi boys' past. He wants to know why Rin would choose to swim in the medley relay instead and why he is so hellbent on defeating Haruka in every race. Haru willingly explains their past to Rei, mentioning the story of Rin's father and the time he beat Rin in a race after he came back to Japan for only a brief while. However, Rei still fails to understand why their friendship would so broken, so the following day he skips out on swimming practice for the finals so he can visit Samezuka to confront Rin with questions himself.
Rin and Rei up in a heated argument involving Rei blaming Rin for why Haru chose to give up swimming and explaining to him how important swimming with his team truly is. Shocked, Rin can hardly fight back and in the end the two part ways, Rin even more disturbed than before. Captain Mikoshiba and even the rest of the Samezuka team can see in Rin's performance during relay practices how he seems distant and disconnected from his relay team; however, no one yet speaks with Rin nor expresses their concern and Samezuka ends up leaving on schedule for finals.
In the city where finals are being held, the Iwatobi team settles down for sleep, though upon receiving a strange message from Rin, Rei ends up leaving his room to meet him atop a hill in the middle of the night. Here, Rin speaks his mind which he did not do when Rei originally spoke to him at Samezuka. Soon, Rin's reasons for his behavior become apparent. He admits Haru's win over him that time they reunited hadn't been the reason he wanted to stop swimming. Instead, he blames himself for not pushing himself harder when he had the chance. In Australia Rin had struggled immensely with all of his races and hardly ever placed high in the ranks. Frustrated, he blamed his history with relays and assumes he might have grown too attached to them during his time in Japan. He never contacted his teammates whenever he would return to Japan because he was too embarrassed to admit to his losses; therefore, Rin grew distant and isolated himself from that past life. Rin eventually ends the conversation telling Rei not to embarrass or let down his team at the finals tomorrow.
Rin arrives back at the hotel the Samezuka students are staying at and Aiichirou informs him Captain Mikoshiba would like to have a brief word. As it turns out, Mikoshiba, concerned about Rin's condition, rearranged the schedule at the last minute to place him once again in the 100 meter crawl rather than the medley relay. Rin appears extremely taken aback by this decision, now worried he truly will never be able to swim with his teammates ever again.
Rin sits despondently in the back of the Samezuka bus on the day of finals with Aiichirou trying his best to encourage him. If anything, the younger boy only irritates Rin even more and he soon storms out to prepare for his race. At the opening assembly, Gou watches on from the viewing bleachers as all the swimming teams gather together. There she spots her brother amidst the other Samezuka swimmers, though he appears listless, tired, and certainly in no condition to be swimming at all. However, Rin still carries on, though during his race he has a late start which earns him a disappointing loss in last place. It is a rare sight to see Rin so tired after a swim and as he struggles to push himself out of the pool Haru abruptly stands from his seat, hoping to find Rin and help him however he can. The rest of the Iwatobi team follow, sacrificing precious time mere moments before their own race begins. Eventually, they hear a loud voice down the hall in the stadium and sure enough find Rin screaming at Aiichirou, proclaiming how terrible he was and how he refuses to keep swimming anymore. Those familiar words rattle the onlookers, though none more than Haru who now fears he will truly never swim with Rin again. Once Rin and Aiichirou have disappeared, Rei admits to his team he spoke with Rin and explains to them what Rin's true feelings are. Rei realizes how badly the three boys want to swim with their friend, so at the last moment he decides to give up his position in the relay provided they can find Rin and persuade him to swim with them one more time.
Check-ins for the medley relay begin just as the boys rush out of the stadium in search of Rin. Haru eventually finds him standing beneath a large tree, its branches bare but stretched out wide towards the sky. Rin is clearly emotionally unstable when he speaks to Haru and even orders him to laugh at him just as the rest of the world supposedly is at his embarrassing failure. Haru refuses and instead tries to reason with Rin by explaining how he now understands what he swims for: his team. In disbelief and perhaps not wanting to listen, Rin charges at Haru, grabbing him by the collar of his jacket as he yells at him to keep quiet. Again, Haruka refuses which only angers Rin further and soon the two go tumbling to the ground as Haru narrowly blocks Rin's incoming punch. The two struggle for only a brief moment, lashing out before something seems to catch Rin's eye and he pauses; his grip loosens on Haru when he sees that there are words etched into the dirt at the base of the large tree. The words read "For the Team" a phrase which Rin, as a child, had painted on a brick for a school project to represent what matters most to him. Earlier that day just before the tournament, Haru had visited the tree which coincidentally resembles the sakura tree at their old elementary school and written those words into the ground with nothing more than a small twig.
After Haru asks if Rin came to the tree because of its resemblance, tears fall onto his cheek and soon Haruka faces Rin who has broken down in tears above him. Between sobs, goes on to admit all he ever wanted to do was swim with his friends again. Haru gives him a knowing smile, studying Rin's crumbling features for a moment, before Makoto, Rei, and Nagisa appear. Together, they convince their friend to join them in their relay.
With mere seconds to spare, Makoto, Nagisa, and Haru show up to check in for their race and from the bleachers Gou and the rest of their cheering squad remain unaware of their plans. First to swim in Makoto with a backstroke followed by Nagisa with his breaststroke, and just as their supporters note how they are far in the lead, Rin appears at the starting podium, shocking everyone including Captain Mikoshiba and Aiichirou from the Samezuka bleachers. Regardless of the inevitable consequences, Rin prepares for Nagisa to reach his end of the pool before he jumps right in, swimming quickly and fluidly, as if with new purpose. As he swims Rin sees a light underwater and enthusiastically swim towards it, pushing in the last few meters of his crawl so Haru can complete the race. As he looks up, Rin watches in awe at the sight of Haruka diving in above him. Finally, after cheering with his team, Rin watches as Haru touches the wall of the pool first and ends up winning the race for the team. He's no longer able to contain his joy and relief by the time Haru exist the pool, so with open arms Rin races to and embraces his friend as he thanks him for showing him the best sight he could have ever asked for. As the four of them celebrate and hug together again, Rei watches on, commenting on how beautiful all of them truly are.
As expected, the team suffers great consequences for allowing a member of another team to swim in their race and thus the Iwatobi team ends up disqualified and ejected from the tournament. All of them accept their loss without regret, however, and can only smile, knowing that in truth, winning is not what matters the most. Elsewhere on the stadium grounds, Rin bows deeply before his captain and requests he be kicked off the swimming team for his reckless and disappointing behavior. Additionally he apologizes to Aiichirou for snapping at him just before Captain Mikoshiba cheerfully orders him to swim as he did for Iwatobi, but for Samezuka. Rin stays on the team, much to his surprise.
Following the events at finals, Rin regularly swims and hangs out with his friends on the Iwatobi team. He can be seen after hours at their school, standing before Haru, Makoto, Nagisa and Rei as he reenacts the time he had to introduce himself at their elementary school as the new transfer student. Though he still swims for Samezuka, Rin supposedly becomes an honorary member of Iwatobi High School, at least as far as his friends are concerned. Gou and Aiichirou interrupt the boys to drag them out for joint practice and as they all run together towards the pool Haru asks Rin if he still intends to follow his father's dream. Rin responds with confidence, telling Haru he now only wishes to follow a dream of his own.