Illyasviel von Einzbern is a normal schoolgirl in Japan. She lives with her overachieving nice guy older brother Shirou Emiya and her two maids, her parents are perpetually out of the country, and she has fanciful dreams of using magic to make her dreams of love with Shirou come true. Enter fierce rivals Rin Tohsaka and Luviagelita Edelfelt, two Magi who have been sent to Japan by Zelretch the Wizard Marshall, Master of Parallel Worlds, with the powerful sentient Kaleidosticks to collect the mysterious Class Cards and clean up their mess. After getting fed up with their constant infighting, one Kaleidostick, Magical Ruby, senses Illya's fleeting dream of magic and leaves Rin for her, tricking her into becoming a magical girl. Now Illya is being forced by Rin to collect the dangerous Class Cards in her place. But perhaps more dangerous still are Illya's own mysteries that may have unknowingly attracted Ruby to her.

It has been a month since Illya and Miyu became magical girls and sealed all of the Class Cards. Rin and Luvia have been forced to remain in Japan to clean up the aftermath, such as the now-unstable magic in the area's ley lines. While helping with the cleanup, the seal on Illya's mysterious innate magic goes berserk and she loses control of her transformation. By the time she has realized what happened, a mysterious girl who looks eerily like Illya appears, apparently bent on bringing destruction down on the original whose heart she seems to have spawned from, and making matters worse she holds the power of the Archer Class Card, with which Illya holds a special bond, within her body.

Little Illya's life has gotten completely out of hand since the Kaleidostick Ruby granted her the powers of a magical girl. Now a regular beach trip is going to turn into another crazy mystery adventure that she and her friend Miyu will have to unravel.

Illya and the gang have finished their battle against the heroic spirit residing in the eighth class card. They're back in vacation mode again, looking to make the most of what they have left of summer break. But their hopes get crushed in the blink of an eye. An all-too-unrealistic silhouette appears before them when they go to investigate the strange event at Mount Enzō. After a short skirmish, the entire space ends up being warped. Illya wakes up in a wintry Fuyuki City... in a parallel world. This is the world where Miyu was born and raised.