Haruka, who is attending college in Tokyo, meets Asahi again and reawakens his memories from his middle school years, including those of Ikuya. Makoto is working toward a new dream while he is in Tokyo together with Haruka. Rin has an unexpected meeting in Sydney.
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...
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.
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...
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.
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...
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.
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.
Ikuya and Haruka face off in the Individual Medley, mending their middle school rift. Hiyori and Ikuya also make amends, swimming the relay as Shimogami U. teammates against Haruka's Hidaka U. team. Afterwards, Natsuya reunites with Ikuya and apologizes to Hiyori while Hiyori, free to be himself, is comfortable seeing Ikuya spend time with his middle school friends once more.
Isuzu Mikoshiba brings her high school swim team to meet Seijiro's college team and challenges Haruka to a freestyle race. Rin returns to Japan, reuniting with his Samezuka friends. Makoto arrives late to one of Haruka's informal meets only to find he's lost to the freestyle world record-holder, Albert Wahlander.
Rin reunites with Sosuke and learns about his recovery. Rei and Nagisa qualify for Nationals. Influenced by Nao and Ryuuji, Makoto's future path switches from coaching to professional training.
Rin and Haruka break from training to attend the high school National tournament, reuniting with old friends.
The All-Japan Invitational hosts swimmers hoping to qualify for global competition. The character of Kinjou Kaede appears for the first time. The Kirishima brothers race together and find peace. Rin qualifies in the 100m butterfly while Haruka loses his first heat. Afterwards, Rin, Haru and Makoto share their personal goals in a private moment. The following day, Haru's last heat takes place with the outcome unstated.