Even though it has been a year since the Iwatobi High School Swim Club has been created, new members have yet to join the club. Now that Haruka Nanase and Makoto Tachibana are senior students, along with their younger friends Nagisa Hazuki and Rei Ryuugazaki, they have to find a way to attract new members. If not, the club will be forced to close the following year due to a lack of membership. Meanwhile, with impending graduation, it is also time for the seniors to decide their plans for the future. Unlike their friend Rin Matsuoka, the new captain of Samezuka Academy Swim Club who is determined to fulfill his dream of being a professional swimmer, Haruka and Makoto are unsure about what career path they want to take. Further problems arise when an old friend of Rin's, Sousuke Yamazaki, comes to the city to study at Samezuka Academy; the recently scouted swimmer's arrival causes tension in the relationship among him, Rin, and Haruka. [Written by MAL Rewrite]

With the seniors having graduated from high school, the determined swimmers eagerly take on their futures with a dream to fulfill. Now attending Hidaka University in Tokyo, Haruka Nanase unexpectedly runs into Shiina Asahi, an old teammate and friend from his middle school days. Consequently, the troubling memories regarding his middle school swim team resurface, as it was a time when Haruka's views on swimming became negative and led him to quit the team. Haruka later reconnects with his other middle school classmates; all except for Ikuya Kirishima, who still resents Haruka for quitting the team, resulting in its disbandment. Aware of the issues between them, Haruka resolves to improve his friendship with Ikuya. However, he quickly realizes that making amends with an old friend isn't his only obstacle. Facing the reality and challenges of encountering higher calibre swimmers, Haruka must work hard to establish himself if he dreams of competing on an international level. [Written by MAL Rewrite]

Taking place between the events of Free!: Eternal Summer and Free!: Dive to the Future, Free!: Take Your Marks plays out the graduated seniors' last summer through four different stories before they set sail for the future. Unmei no Choice! (Destined Choice!) follows Haruka Nanase and Makoto Tachibana searching for a new apartment for Haruka as he settles into Tokyo. Hitou no Cooling Down! (Cooling Down at the Secret Hot Spring!) sees Aiichiro Nitori choose a graduation gift for Rin Matsuoka and Sousuke Yamazaki, while Momotaro Mikoshiba wins tickets to the Anago Hot Springs. Hoping for a trip together, Aiichiro and Momotaro invite Rin and Sousuke. Kessoku no Batafurai! (United Butterfly!) shows Rei Ryugazaki, Nagisa Hazuki, and Gou Matsuoka creating a recruitment video to attract new club members for the next school year. Tabidachi no Etanaru Buru! (Departing Eternal Blue!) looks into the Iwatobi and Samezuka swim teams' plans for Rin's surprise going-away party, as he will be departing for Australia soon. [Written by MAL Rewrite]

After the accident in which she lost her mother, 16-year-old Tooru moves in with her grandfather, but due to his home being renovated, is unable to continue living with him. Claiming she will find someone to stay with but also fearing the criticism of her family and not wanting to burden any of her friends, Tooru resorts to secretly living on her own in a tent in the woods. One night on her way back from work, she finds her tent buried underneath a landslide. Yuki Souma, the "prince" of her school, and his cousin Shigure Souma, a famous author, stumble across Tooru's situation and invite her to stay with them until her grandfather's home renovations are complete. Upon arriving at the Souma house, Tooru discovers their secret: if a Souma is hugged by someone of the opposite gender, they temporarily transform into one of the animals of the zodiac! However, this strange phenomenon is no laughing matter; rather, it is a terrible curse that holds a dark history. As she continues her journey, meeting more members of the zodiac family, will Tooru's kindhearted yet resilient nature be enough to prepare her for what lies behind the Souma household's doors? [Written by MAL Rewrite]