During a regular after-school grub crawl, gluttonous high schooler Hibiki Sakura is confronted about her ever-expanding waistline by her best friend, Ayaka Uehara. With her attempts at solitary exercise failing miserably, Hibiki decides to join the newly opened Silverman Gym. At her orientation, Hibiki runs into student council president and school idol Akemi Souryuuin. However, it soon turns out that Hibiki is in for a lot more than she bargained for. Not only is Silverman Gym full of world-renowned bodybuilders and athletes, but to make matters worse, Akemi turns out to be a total muscle fetishist! Grossed out by the scene unfolding before her eyes, Hibiki begins to leave, only to be stopped by trainer Naruzou Machio. Completely enthralled with her newfound Prince Charming, Hibiki signs up as a gym member. Now, as a result of her spur-of-the-moment decision, Hibiki must adapt to her new lifestyle.

Waking up to find herself in a parallel version of Fuyuki City, Illyasviel Illya von Einzbern is lost and alone. She discovers her home in ruins, with a massive crater lying in the center of her hometown. With snow falling in the middle of summer, confusion consumes the young elementary schooler, who has no knowledge of where her friends or her wand Ruby may be. Making it to the remains of her house, she is suddenly tackled by an amnesiac girl. Wearing a gym uniform as the icy temperature sets in, the mysterious girl has no idea of where she is or why she showed up. However, this stranger, known as Tanaka, apparently has information about the location of Rin Toosaka, Miyu Edelfelt, and the rest of Illya's missing friends. Fleeing from agents of the Ainsworth family⁠—those in control of this parallel realm—where will these two end up, and how will Illya restore the present back to the world she once knew?

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.

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?