The story revolves around Haruka Nanase, a boy who has always loved to be immersed in water, and to swim in it. Before graduating from elementary school, he participated in a swimming tournament along with his fellow swimming club members, Makoto Tachibana, Nagisa Hazuki, and Rin Matsuoka. After achieving victory, each of the boys went their separate ways. Time passed, and in the middle of their uneventful high school lives Rin appears and challenges Haruka to a match, showing Haruka his overwhelming power. Not wanting it to end like this, Haruka, gathers together Makoto and Nagisa once again and brings a new member named Rei Ryugazaki to create the Iwatobi High School Swimming Club in order to defeat Rin.
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...
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