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 is now attending Samezuka Academy upon his return from Australia. 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.
After the match, Haruka and the others are 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 home room teacher, Miho Amakata who agrees after they give her a little prompt. While continuing the restoration, Gou, who was still confused about Rin's behavior, asks Makoto about their race and learns that Haruka threw the match. Believing that they can revert Rin to his old self, Gou volunteers to join the club as their manager. Later, Makoto pays one final visit to the Iwatobi Swimming Club and runs into their old mentor, Coach Goro Sasabe.
Upon learning why Haruka quit competitive swimming, Makoto calls Rin to inform them of their plans while Rin decides to join the Samezuka swim team for his own grudge against Haruka.
Nagisa and Makoto try teaching Rei how to swim after his innumerous unsuccessful attempts to do so and learn that while he can float, his problem still eludes them. Makoto then suggests they ask Sasabe for help but he bluntly refuses.
The club tries and fails to get Miho to sponsor the trip to the island where they wanted to train for the next swimming tournament. Makoto proposes using camping equipment to stay outdoors while resorting to bribing Sasabe to use his squid fishing boat to take them to the island and back. 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.
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.
Haruka gets Makoto out of the water and falls down out of tiredness. He finds out that Makoto is alive, but his heart beating is slow. After checking if Makoto is injured, he decides to perform CPR, but when his mouth is about to touch Makoto's, Makoto suddenly wakes up and finds worried Haruka beside him.
In this scene, we see Makoto and Haruka's relationship in greater depth. Haruka shows his completely raw and vulnerable side for the first time, and this is because of how scared he is of losing Makoto. Haruka, who never says anything louder than necessary, also shouts for the first time in this scene, calling for help to come. It is often thought that Haruka is impassive and blank, but we see a torrent of emotions washing through him as he looks at Makoto's nearly lifeless body.
After Makoto regains conciousness, Haruka asks Makoto if he's still afraid of the ocean, which Makoto answers "I thought I'd gotten over it.". Makoto apologizes to Haruka for dragging him into all that and says that all he wanted to do is to swim with Haruka once again. Haruka gets a surprised look on his face just when Nagisa and Rei appear running toward them. Makoto runs to them and apologizes to Rei for not being able to save him, but Rei then tells him that he's the one who should be sorry for making them worry. 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 gonna stop soon. Makoto tells him that it'll be hard for them to sleep because of the situation they're in. Rei then asks Makoto why was he acting strange when he tried to save him, but Haruka interferes saying that they're not going to discuss that. Makoto, however, says that that's okay and tells the group a story about a fisherman and his goldfish. Soon after he finished his story, the rain stopped and the group went outside to see a beautiful sky above them. 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.
As Gou and Makoto watch Haruka and Nagisa swim, Gou states that Haruka's time have improved 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.
As Makoto, Nagisa and Rei go to check on Haruka if he's okay, they seem to run into Rin in the hallway. Nagisa asks him if he saw Haru anywhere, but Rin just smiles and asks them if losing to him was that big of a shock to Haruka. Makoto interferes and says that there actually is something more, that at least Haruka thought so and that that was probably the reason why he wanted to race with Rin. Rin tells him that nothing else than beating Haruka matters to him and leaves. The group decides to go and prepare themselves for their own races.
Back to the competition, 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 to find Haruka. When Nagisa and Haruka arrive at the pool, Haruka sees Goro, Miho, Gou and Rei cheering for Makoto and Makoto swimming his last sprut. He stands there speechless as Makoto finishes the race being second. As he gets out of the water, he sees that Haruka was watching him swim and smiles warmly.
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.
They go to Haruka's house with a 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. Rei, Nagisa and Gou leave him a voice message, but soon discover by Makoto that he doesn't bring his phone with him often.
After some time, Haruka finally comes back home, just to find Makoto sleeping on the doorstep of his house, holding his phone. He takes it and listens to a voice message Nagisa, Rei and Gou left him a while ago. He looks at Makoto sleeping and remembers the words he said to him when he rescued him from the ocean and decides to wake Makoto up. Makoto wakes up finding Haruka in front of him asking him if they have a relay to swim the other day and blushes out of joy. This can also be considered a push in Haruka's feelings as he is starting to think more and more about Makoto and his feelings towards Makoto.
Thanks to everyone's efforts, Iwatobi manage to win the relay race, earning a place in the regionals. Later, the group attend a summer festival, where Haruka tells Makoto how much he and others made him happy and that he wants to swim in the relay with others again, much to Makoto's joy. Anime director Hiroko Utsumi has called this Haruka's confession in interviews, stating "... I think that Makoto is very important to Haruka, and this can be called the second confession..."
Later that night, Haruka tells Rei a story about Rin's obsession on swimming relay, which Makoto and Nagisa listen to as well.
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 rooms, the group go to see the pool they'll be swimming in. Haruka thanks to Makoto for always being there with him. In an interview of the anime production team, a storyboard manager stated that "Makoto is very important to Haruka, and Haruka doesn't show his feelings very often, so when he does, he truly means every word."
After Rin runs off in an outburst, telling Aiichiro that he will quit swimming, Haruka, Makoto 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.
Later, 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. The episode ends with showing Haruka, Makoto, Nagisa, Rei and Rin's photo after winning the tournament.
Makoto hurriedly gets ready and goes to pick up Haruka to meet Nagisa and Rei at a bus station. The swimming team arrives at Samezuka Academy, where the Samezuka was having a third-year's send off race. Seijuro Mikoshiba asks them if they would like to have a race between Iwatobi vs. Samezuka, a freestyle medley relay. Iwatobi ends up loosing, much to Nagisa and Rei's frustration. Along with his teammates, Makoto is surprised that Rin is going to be the new captain.
The next day, the Iwatobi High School holds an assembly about the clubs there for the new-coming, first-year students. When the Iwatobi Swim Club's presentation comes up, Nagisa and Rei becomes worried but Makoto says that they should trust Gou. Unfortunately, the Iwatobi Swim Club doesn't get any new members. They didn't give up and decides to go ask their supervisor, Amakata's help. Amakata gives them an advice to ask Coach Sasabe, if they could use the swimming pool there.