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.

Hundreds of years ago, the Chinese zodiac spirits and their god swore to stay together eternally. United by this promise, the possessed members of the Souma family shall always return to each other under any circumstances. Yet, when these bonds shackle them from freedom, it becomes an undesirable burden—a curse. As head of the clan, Akito is convinced that he shares a special connection with the other Soumas. While he desperately clings to this fantasy, the rest of the family remains isolated and suppressed by the fear of punishment. Tooru Honda, who has grown attached to the Soumas, is determined to break the chains that bind them. Her companionship with the family and her friends encourages her to move forward with lifting the curse. However, due to confounding revelations, she struggles to find the tenacity to continue her endeavors. With time slowly withering away, Tooru contends with an uncertain future in hopes of reaching the tranquility that may lie beyond all this commotion.

A year has passed since Tooru Honda began living in the Souma residence, and she has since created stronger relationships with its inhabitants Shigure, Kyou, and Yuki. She has also grown closer to the rest of the Souma family and has become familiar with their ancestral secret, having helped them with many of their personal issues. The closer Tooru gets, however, the more she begins to realize that their secret holds a darker truth than she first presumed. Summer is approaching and Tooru is invited to spend her days with the Soumas, mainly Kyou and Yuki. Tooru wishes for an easy-going vacation, but her close relationships with the two boys and the rest of the Soumas may prove to cause trouble. As they grow more intimate, their carefree time together is hindered by older hardships and feelings from the past that begin to resurface. The Eternal Banquet also dawns on the members of the zodiac, and they must tend to their duties alongside the unnerving head of the family, Akito Souma. With the banquet approaching and a plethora of feelings to be solved, will Tooru's life with the Soumas remain peaceful, or will she find herself in a situation from which she cannot escape?

Ever since the 10th NOVA clash, the Chevalier had concluded that the NOVA have been appearing at a steadier rate and they are losing more Pandoras than they can produce. Their solution is the E-Pandora Project which involves normal humans being given the power to become Pandoras. Inviting Pandora from around the world to their Alaskan base witness the unveiling of their new project, Satellizer, Kazuya and Rana are among those who have been summoned. However, as time goes the E-Pandora Project starts to become fishier and the Pandoras start to grow more and more concerned...