Illyasviel Von Einzbern, or Illya for short, is an ordinary girl living in Fuyuki City. One day, while she's taking her bath at night, a suspicious magical stick, "Magical Ruby" suddenly flies in, and tries to tempt Illya into becoming a magical girl...?!

Illya gets dragged into becoming magical girl, but she decides what's done is done and tries to be positve as she practices her magic. However, her practice was all just Ruby teasing her. And so, Illya is forced to handle her first mission without knowing how to use any magic...

A mysterious girl, Miyu, suddenly appears when Illya falls into a pinch on her first mission. Miyu then transfers to Illya's school, but not only does she fail to get along with her new classmates, she seems to be against fighting alongside Illya. However, the place Miyu moves into is right in front of Illya's house?!

The two teams: Illya and Rin, and Miyu and Luvia head to the riverbed to collect the next Card and face off against Caster. Because Caster is high up in the air, Illya and Miyu have to learn how to fly in order to defeat her. Illya is able to fly with ease, but Miyu has a difficult time.

Illya and the others are attacked when Saber suddenly appears. In order to rescue Rin and Luvia who suffered severe injuries while caught off guard, Illya and Miyu fight together. However, Illya's still not used to fighting, making it hard for her to face Saber, and she gets caught in a predicament. What strategy does Ruby have to save the day?!

It looked like Rin and Luvia's attacks had managed to defeat the Class Card, Saber, however, they failed to deliver a fatal blow, and everyone faces a counterattack from Saber's Noble Phantasm, Excalibur. When Illya receives an attack boasting such unprecedented power, a sudden change occurs?!

Everyone managed to pull through somehow, but the next day Illya comes down with a high fever from the strain. Illya takes the day off of school to rest along with Miyu who calls her through Sapphire and Ruby's video phone. But when Illya sees Miyu in her maid uniform, she...

When Illya recovers her memory during the fight with Assasin, she suffers shock, and grows hesistant to talk to anyone, even Miyu. Now that Illya truly understands the cost and meaning of being a magical girl, she feels terrified and after deep consideration she goes to speak with Rin.

Miyu, Rin, and Luvia head to the Mirror World to defeat the final Class Card, Berserker, however they're all having a hard time against Berserker's almost invincible power. Meanwhile, Illya is feeling down as she bathes after running away from being magical girl when her mother, Iri bursts in on her?!

Even after drawing out the Class Card's true power and managing to damage Berserker, Miyu is still facing a difficult battle. But Illya enters her Trance and comes running to save Miyu from her pinch! Though Berserker, their greatest enemy yet, still stands before them, when the two Kaleid Liners combine their power, a miracle occurs!