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.

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.

As prefecturals draw near, Haruka and the other swim club members continue to improve. Meanwhile, Rin reveals his motivations for swimming. The swimmers must now show what they have accomplished at the tournament.

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.

Haruka and his friends have grown after last summer’s tournament. Amidst the hustle and bustle of training for their individual events, their daily lives continue as usual. However, a new season now approaches!

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…

The members of the Iwatobi Swim Club ponder over the cause of Nagisa’s odd behavior at the end of practice that day. Though they time their chance well to ask Nagisa what’s happened, Nagisa stubbornly refuses to explain why he’s upset...

While Haruka and the boys redouble their training in the wake of prefecturals, Makoto notices Gou looking troubled and asks her what’s wrong. She tells him that Coach Sasabe has been so busy with his Swim Club lately, he hasn’t been by to approve their new training regimen. Makoto offers to go see him for her, but what he finds at the Swim Club is...

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.

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...

Having faced his feelings honestly at last, Haruka tells Makoto, Nagisa, and Rei what he has decided for himself and his future. The Iwatobi Swim Club is once again fully united as they mount the starting block at nationals, ready to swim for themselves, for their friends, and now, for the future as well.

Haruka has entered Hidaka University, where he's now training with the swim club to prepare for a newcomer tournament. One day, he runs into Asahi, a swim teammate from middle school. Haruka is later joined by Makoto, who also moved to Tokyo, at a coffee shop to catch up with Asahi... and the topic quickly turns to Ikuya, another teammate they swam with in middle school. On the day of the newcomer tournament, Haruka and Asahi are in the same race for the first time in years... and the spectacle is watched by Hiyori, who calls Haruka an "inferior copy of Ikuya." After the race, as Haruka is walking through the halls with Asahi, he catches sight of Ikuya passing by..

Rin, now living in Australia, trains hard every day with swimmers from all around the world. Then a Japanese guy shows up where his team is training, challenging each of his teammates to races and beating them one by one. Even Rin is surprised when this newcomer reveals his identity...

The Iwatobi High School Swim Club is participating in a joint training camp with the Samezuka Academy and Soufuukan High School teams. Sousuke is also participating as an alumnus. In the midst of the excitement, Rei and Nagisa notice that something is odd about Romio's swimming. Then Shizuru tells them the story of what happened to Romio in middle school...

With the college championships approaching, all the swimmers are training hard on their own in addition to their official club practices. Haruka is also undergoing some extra training, with coaching from the mysterious man they've been seeing around campus. Makoto is concerned about the arrangement, but Haruka assures him that he asked for the help himself

Haruka's next race is the All-Japan Invitational, which determines who will represent Japan at the global level. To prepare for this important tournament, Haruka is invited to a special training camp.

Makoto meets up with the members of the Iwatobi Swim Club who are in Tokyo for the nationals. Meanwhile, Haru continues his training.