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]

Mage's Association members Rin Toosaka and Luviagelita "Luvia" Edelfelt are tasked with finding and retrieving seven Class Cards, medieval artifacts containing the life essence of legendary Heroic Spirits. To aid them in their mission, they are granted the power of Ruby and Sapphire, two sentient Kaleidosticks that would enable them to transform themselves into magical girls and drastically increase their abilities. However, the two mages are on anything but good terms, prompting the Kaleidosticks to abandon them in search for new masters. They stumble upon two young schoolgirls—Illyasviel von Einzbern and Miyu—and quickly convince them to form a contract. With their new powers and responsibilities, Illya and Miyu set forth to collect all the Class Cards. [Written by MAL Rewrite]

Another lovely summer goes by for Illyasviel von Einzbern. Taking a break from her magical girl duties, she enjoys her time off after collecting the Class Cards with her best friend Miyu Edelfelt. However, her break comes to an abrupt end when she and Miyu are abducted by Rin Toosaka and Luviagelita Edelfelt, while out with her friends. The magical girls learn that their work is far from over, as Clock Tower informs them that the out of control mana thought to have been sealed continues to be dispersing throughout Fuyuki City. After heading to the origin point of the out of control mana, Illya and Miyu are tasked with solving the anomaly. But after casting their spell, Illyasviel discovers that she's split into two people! As this mysterious new form darts off, she can only wonder: what is to come from the existence of her dopplegänger, running amok in the unsuspecting town? [Written by MAL Rewrite]