A compilation movie of the TV series containing a newly added footage.

Rin Matsuoka’s childhood friend, Sousuke Yamazaki, has recently transferred to Samezuka Academy. Upon their reunion, the two reminisce about their childhood days and reaffirm their wish to swim together. Now with Rin, Sousuke, Captain Mikoshiba’s younger brother Momotarou Mikoshiba, and hard-working Aiichirou Nitori, the Samezuka relay team is formed, and their friendship deepens. However, as tournaments, races, and training go on, the reason for Sousuke’s sudden return begins to trouble him and affect his swimming. Noticing Sousuke’s change, Rin pushes to uncover what is holding him back.

Haruka Nanase has reconciled with his rival Rin Matsuoka, and they have re-established their friendship, determined to race each other again. Now Haruka, along with Makoto Tachibana, Rei Ryuugazaki, and Nagisa Hazuki, prepare for their upcoming tournaments, determined to compete wholeheartedly and achieve victory as a team. At Samezuka Academy, Rin resolves to do the same. Further, the seniors near graduation, and Rin has decided his future plans. However, Haruka and Makoto remain uncertain, and they begin to feel the pressure of having to choose their own paths.

The story takes place on an island, where a Fractale System is beginning to collapse. One day, Clain finds an injured girl called Phryne under a cliff. She disappears leaving a pendant. Clain sets out for a journey with the girl-shaped avatar Nessa to look for Phryne and discovers the secret of the Fractale System.