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.

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.

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.

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.

Coach Sasabe begins training the Iwatobi Swim Club for the upcoming tournament. Meanwhile, Rei is unhappy about the fact that he's the only one who doesn't know about what happened with Rin in the past. After Rin expresses his frustration, Haruka decides to tell him about what happened when they were in grade school.

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 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

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 Iwatobi Festival has begun! Haruka and friends are fired up for the Club-versus-Club Relay Race, hoping to attract new members by putting in an impressive performance. Meanwhile, Rei begins training but is worried by the fact that he can still only swim the butterfly stroke…

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...

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...

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?

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...

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.

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...

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.