At the start of a new school year, Haruka and the others meet up with Rin at Samezuka Academy for an event to send off the third year members, where they end up getting roped into a freestyle relay against the school. Afterwards, as the Iwatobi Swim Club struggle to recruit new members, Goro reveals he has reformed the Iwatobi Swimming Club, giving the guys a chance to use the indoor pool prior to its opening. Later, Rin, who has been made captain of the Samezuka Swim Club, participates in a race against Haruka, managing to tie for the lead. Later that evening, Haruka and the others invite Rin to the school pool, which they have cleaned and filled with cherry blossoms so that Rin could swim in it, only for rain to ruin the opportunity. The next day, Rin is surprised to find an old acquaintance of his, Sousuke Yamazaki, transfer into his class

Rin reminisces with Sousuke, his classmate prior to transferring to Iwatobi during elementary school, who decided to spend his last year of high school in his hometown before swimming professionally. Meanwhile, Goro plans to put on a swimming festival for the Iwatobi Swimming Club for children, asking Haruka and the others to spread word and come up with a main event, with Haruka suggesting a relay event. With Rin asked to assemble a team of his own to swim against them, Sousuke asks to join on the condition he run in the freestyle leg. On the day of the event, one of Rin's team members is forced to drop out, but they manage to find the former team captain's brother, Momotarou Mikoshiba, to fill in for him. Prior to the relay, Sousuke confronts Haruka, telling him not to get in Rin's way. As the relay gets underway, both teams show strong form with Haruka's team narrowly managing to win.

The Iwatobi Festival has begun. Haruka and his friends are excited to get new members by showing a cool place at the club activity counter relay

With the prefecturals approaching, Gou takes it upon herself to make balanced nutritional bento lunches for the team. Meanwhile, Sousuke recalls a promise that he had yet to ask of Rin before he left for Australia, before asking Rin what happened whilst he was away, hearing about how Haruka and the others helped pick himself up. When Gou's attempt at a nutritional bento proves to be effectively inedible, she compensates by putting together a tough training regime. Later that night, Sousuke tells Rin he should give up relays in order to focus on his dreams, but Rin states his determination to accomplish both. Despite having always preferred swimming individually, Sousuke asks to join Samezuka's relay team in order to find something he's missing, challenging Rin to a butterfly race to earn his spot. Admiring Sousuke's passion, Rin changes the way swimmers are selected for relays, asking only those who are serious about being in a relay team to step forward.

After the others notice him behaving oddly and insisting on sleeping over, Nagisa reveals he has run away from home, eventually explaining that his parents told him to quit the swim club because of his poor grades. Wanting to avoid his mother, Nagisa and the others hide out at the swimming center to come up with a plan, where Nagisa laments how he doesn't find studying fun, having been forced to do it endlessly during middle school. As the group move further into the school when someone approaches, Rei tries to convince Nagisa to tell his parents how he really feels. Moved by everyone's words, Nagisa vocalises his true feelings to the pursuer, who turns out to be their teacher, Miho Amakata, who came after Haruka told her to let them handle it and gives Nagisa the courage to talk to his parents.

On the day before the prefecturals, Rin and Gou pay their respects to their father, where Rin gives Gou a photo of him to put up in the Swimming Club. The next day, Nagisa, Makoto, Rei, Rin, and Momotarou all qualify in their respective individual events. Later, Makoto competes against Haruka in the 200m freestyle, wanting to have a real race against him before he graduates. Despite losing due to his pacing, Makoto feels happy to have been able to have a serious race with Haruka. Haruka and Rin then face off against each other in the 100m freestyle, with Haruka narrowly beating Rin by a split second, bringing the first day's events to a close.

After Rin choose his team for the medley relay event, which includes Sousuke and Momotarou, Nitori feels downhearted over not making the team, but receives some encouragement from Sousuke. The next day, as the relay gets underway, Samezuka manages to win the race, though Iwatobi manage to make it through to the regionals as well. Afterwards, as Haruka and Rin are both scouted, Rin confronts Sousuke about his recent behaviour, to which he responds that he hasn't yet found what he is looking for. After receiving some encouragement from Rei, who tells him to be true to his 'free' self, Haruka comes up with a training regime to improve their relay times. Later, Gou spots Sousuke as he skips his team practise.

Makoto starts helping Goro at the Swimming Club, acting as a coach teaching children to swim. Meanwhile, Sousuke decides to help coach Nitori to improve his swimming. As Makoto notices one of his students, Hayato, struggling with swimming without a kickboard, he discovers his brother is Kisumi Shinigo, an old classmate from his and Haruka's middle school. As the two reminisce, Kisumi explains to Makoto how Hayato developed a fear of swimming after he nearly drowned after falling off a boat. Told by Haruka to think over his own experiences of learning to swim, Makoto teaches Hayato how to do a backstroke, helping him to overcome his fear. As Makoto's time as a coach comes to an end, he and Haruka learn from Kisumi that Sousuke had recently obtained an injury to his shoulder and had been competing in tournaments in spite of it.

On the day before the regionals, both Iwatobi and Samezuka end up staying at the same hotel. While Nitori is chosen to swim in Samezuka's relay team thanks to his training, Haruka, who is in deep thought about being scouted, ends up sharing an elevator ride with Sousuke, confirming his shoulder injury. The next day, as Rin manages to pass his heat in the 100m freestyle, Haruka becomes overwhelmed by the pressure of performing in front of scouts and ends up stopping dead in his tracks. When Rin confronts him following the race, Haruka snaps at him, feeling that stuff like dreams and his future are being forced upon him. As Haru tries to assure his friends he will swim in the relay with them, Sousuke continues to experience more pain from his shoulder injury.

After being informed by Nitori, Rin becomes aware of Sousuke's shoulder injury, learning that he had been harboring for two years and that all his talk of being scouted was a lie.

As both Iwatobi and Samezuka continue to train for the nationals, Rei worries about Haruka, who is unable to participate in the freestyle event. Later, Haruka is approached by Sousuke, who tells him to move forward so that Rin can improve alongside him. As Obon arrives, Makoto and the others confront Haruka that he isn't being his usual 'free' self, expressing their desire to help him find a dream. However, Haruka refuses to hear Makoto out, becoming further upset when he reveals he plans to go to a university in Tokyo. As Haruka starts to seclude himself, he is approached by Rin, who decides to take him with him to Australia.

Upon arriving in Australia, Rin takes Haruka to the beach, where he talks about his experiences in the country before taking him to meet his homestay parents, Russell and Lori. Upon checking into their hotel, the pair find they have to share a double bed for the night, though they manage to get through the night reminiscing about their time together. The next day, Rin takes Haruka to Sydney's Aquatic Center to swim alongside Australia's national swim team, reigniting Haruka's passion for swimming. As Rin states he came to Australia to approach his old coach about joining his team, Haruka states he has also found a dream to aim for.

Upon returning from Australia, Haruka gives his thanks to Rin and rejoins his teammates, deciding that he will start focusing on times and winning for the sake of reaching his new dream to swim in the wide open world. He then apologises to Makoto, who explains he is going to a Tokyo university in order to become a swimming teacher. On the night before the national tournament, the group reminisce about the past two years together, with Nagisa and Rei becoming emotional about Haruka and Makoto's impending graduation, though Haruka assures them will always be connected. Following a memorable experience at the nationals, in which Iwatobi manage to win, it is graduation time. Rin passes on the position of Samezuka's captain to Nitori, before telling Sousuke that he'll wait until he returns to the world of swimming.