Four boys named Haruka, Makoto, Nagisa and Rin all participated in a swimming tournament shortly before graduating elementary school and later parted ways. Years later, they reunite when Rin challenges Haruka to a race and wins. Not wanting to be defeated so easily, Haruka gathers Makoto and Nagisa and a new recruit named Rei to form the Iwatobi High School Swimming Club.

The Iwatobi Swimming Club is back and struggles with the recruitment of new members. At the same time, senior members Haru and Makoto have to figure out what to do after high school, challenging their love for swimming. Meanwhile an old childhood friend of Rin returns and stirs up some trouble - especially with Haru. How is the Iwatobi gang going to respond?!

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.