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.

The Iwatobi Swim Club must win to advance to nationals. As the tournament draws near, the members get nervous. Meanwhile, Rin grows increasingly irritated. As it comes time for the medley relay, each member must find their own answer as they step up to the start line

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.

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...

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.

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

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...

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.

At Samezuka Academy, the hot-blooded practices continue ahead of regionals. Meanwhile, the Iwatobi Swim Club trains diligently each day until sundown. Though Amakata-sensei is concerned, Haruka and the boys insist they want to practice as much as possible before the tournament.

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…

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.

There's trouble at the beach. The four swim club members are forced to revisit their motivation to swim. After Rei asks Makoto about his odd behavior during the training camp, Makoto tells them about his past.

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!

On the eve of prefecturals, Makoto resolves himself to broach a certain subject with Haruka. As the tournament begins, the Iwatobi Swim Club is extremely enthusiastic about its prospects. But will every member be able to pass the prelims of his individual events?

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 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.

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?

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...

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.