"Free! -Take Your Marks-" is a sequel film to the "Free!" anime series, serving as a bridge between the second and third seasons. The narrative centers on the Iwatobi High School swim team members—Haruka Nanase, Makoto Tachibana, Nagisa Hazuki, and Rei Ryugazaki—as they navigate the transition from high school to their future paths. The film is divided into four interconnected segments, each focusing on a different character or group dynamic.

The first segment revolves around Haruka and Makoto as they search for a new apartment in Tokyo, where they plan to attend university. Their journey highlights their close friendship and the challenges of adapting to a new environment. The second segment focuses on Nagisa and Rei, who are tasked with organizing a farewell party for their upperclassmen. Their efforts to create a memorable event underscore their camaraderie and the bittersweet nature of parting ways.

The third segment shifts to the former Samezuka Academy swimmers, Rin Matsuoka and Aiichiro Nitori, as they prepare for their own futures. Rin grapples with the pressure of living up to his family's expectations while pursuing his swimming career, and Aiichiro reflects on his growth as a swimmer and his bond with Rin. The final segment brings all the characters together for a nostalgic trip to their old swimming club, where they reminisce about their shared experiences and reaffirm their commitment to supporting each other.

Throughout the film, themes of friendship, growth, and the passage of time are explored, with each character confronting the uncertainties of adulthood while cherishing the bonds they have formed. The narrative maintains a balance between lighthearted moments and emotional depth, capturing the essence of the series' focus on personal and collective journeys. The film concludes with a sense of optimism, as the characters look forward to their futures while holding onto the memories and connections that define their past.