After spending their first year of high school in peace and quiet, Haruka and Makoto run into Nagisa, a new student who was a member at a swimming club with them when they were kids. That swimming club is being torn down, so the three of them sneak in to dig up a time capsule that they buried in the back, which is when they are reunited with Rin, the fourth member of their group who left to study abroad.

Makoto and Nagisa watch with their breaths held as Haruka and Rin engage in an intense race. However, they notice that Rin appears to be have changed. At the same time, Nagisa prepares to start up a swim club with help from Rin's sister Gou.

The Iwatobi Swim Club needs one more member before it can participate in relays. Nagisa has set his sights on his classmate Rei, who is a member of the track team. Despite Rei's refusal to join, but Nagisa appears intent on recruiting Rei into the swim club.

The Iwatobi Swim Club has a full roster now.As they begin to practice, they run into a little trouble.After a certain member claims that his swimsuit is to blame, the club makes a trip to buy new swimsuits.

Haruka and the other club members decide to hold a training camp to prepare for prefectural. Each member follows his own regimen. However, Rei is unhappy about falling behind and heads back into the ocean at night to practice.

Haruka, Makoto, Nagisa, and Rei swim in their individual events. Rin becomes irritated as he remembers watching them swim back in grade school. Afterwards, the four Iwatobi Swim Club members must prepare for the medley relay.

Prefecturals are over and the Iwatobi Swim Club members are pleased by the progress they have made. A local summer festival gives them an opportunity to relax. When Nagisa finds out that Rin is also at the festival, he orders Rei to follow Rin and make sure that Haruka and Rin do not meet.

After hearing about what happened in the past, Rei goes to Samezuka Academy to ask Rin what he wants. The night before Iwatobi and Samezuka leave for regionals, Rin calls Rei to explain how he feels about the relay. And then, Samezuka announces its lineup for the relay.

The crew ponders how to attract new members to the Swim Club. Haruka is called in by Amakata-sensei to discuss his intended career path, but as always, Haruka moves to the beat of his own drum. Meanwhile, Coach Sasabe brings an interesting opportunity to the boys…

In anticipation of the upcoming prefectural tournament, the members of the Samezuka Swim Club enthusiastically show off their individual abilities. At the Iwatobi Swim Club, an equally enthusiastic Gou proposes a lunchbox inspection to ensure the boys are getting the right nutrition to support their training. However...

Haruka and the boys have trained hard to prepare for this showdown against Samezuka. After Day 1 of the tournament, Gou and Amakata-sensei treat the boys to a fabulous, carb-rich feast and allow them to take a breather. Meanwhile, Rin is faced with a tough decision as captain of the Samezuka Swim Club. Who will he choose to swim the relay with him?

As the tournament continues, Sousuke finally tells Rin about how he’s passed their years of separation. Rin is concerned at Sousuke’s nonchalant attitude toward certain things and tries to speak his mind. Meanwhile, the Iwatobi Swim Club looks toward the relay final.

The Iwatobi Swim Club continues their training. However, signs of confusion seem to keep surfacing in the silent Haruka’s swimming. Makoto and the others are worried about him, but try to continue acting cheerfully as though nothing was wrong. But one day, Sousuke appears, asking to speak to Haruka…

Upon Rin’s invitation, Haruka finds himself venturing to “a certain country.” Knowing that Haruka has hit a wall worrying about his future, Rin opens up and speaks to him about his own thoughts and feelings. Afterward, Rin quietly asks Haruka what he will do about his own future...

Haruka and his relay teammates decide to hold a training camp in the summer of their second year of middle school. During the night, Haruka heads out to the pool and finds Ikuya looking up at the stars.

Haru, Makoto, and Asahi visit Shimogami University in hopes of talking to Ikuya, but even after looking all over campus, they can't find him. Hiyori, however, notices them and makes it his mission to keep them from seeing Ikuya.

Hiyori still remembers the first time he saw Ikuya smile. Both boys grew stronger through rigorous training while they studied abroad in America... but seeing Haruka threw Ikuya off his stride. Now Hiyori wishes Ikuya would just forget about Haruka for good.

After the breakup of his middle school swim team, Ikuya decided to get stronger on his own and not rely on anyone. But Haruka, breaking out of his freestyle comfort zone to swim in the individual medley, tells Ikuya that he's not alone.

Makoto has been unable to get in touch with Haruka following the friendly race at his training camp, making him worry that Haruka is dwelling on what happened. Then Nao approaches Makoto to tell him about a rumor he heard.

Nagisa, Rei, and the rest of the Iwatobi Swim Club have come to cheer on their former teammates at the All-Japan Invitational. Makoto tells them the story of how ever since Haruka swam for the first time, he'd been swimming only freestyle.