In the backwater town of Bellforest lives a 14-year-old boy named Renton Thurston. He desires to leave his home behind and join the mercenary group known as Gekkostate, hoping to find some adventure to brighten up his mundane life. However, stuck between his grandfather's insistence to become a mechanic like him and the pressure of his deceased father's legacy, the only excitement Renton finds is in his pastime of riding the Trapar wave particles that are dispersed throughout the air, an activity akin to surfing. Everything changes when an unknown object crashes through Renton's garage, discovered to be a Light Finding Operation—a robot capable of riding the Trapar waves—specifically known as the Nirvash typeZERO. Its pilot is a young girl named Eureka, a member of the Gekkostate, who requests a tune-up for the Nirvash. Their meeting sparks the beginning of Renton's involvement with the Gekkostate as he takes off alongside Eureka as the co-pilot of the Nirvash.

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?