Illya's fun summer break comes to a sudden end. The aftermath of their battle against the Heroic Spirit of the 8th Class Card disappeared overnight from Mt. Enzou. Their suspicions aroused, Illya and the others race to the scene, where they encounter two mysterious women who say they've come to retrieve Miyu... After a fierce battle, they're all bathed in a mysterious light. Afterwards, Illya wakes up to a midwinter Fuyuki City?!

One of Ainswoth's dolls, Beatrice, attacks Illya and the mysterious girl, Tanaka. Both are driven into a corner by her overwhelming strength. Just as they run out of options, someone calls Beatrice back, freeing them from their peril. Afterwards, they both fall victim to hunger and a suspicious ramen shop owner gets them into an even worse crisis--they don't have money to pay him! But the one who saves them from those straits is who you'd least expect.

Led by Gil, Illya and Tanaka successfully infiltrate the Ainsworth mansion. Their goal is the room where Miyu's held captive, but standing in their way is Beatrice and Angelica. When she's driven into a corner, Illya manages to reunite with Magical Ruby, regaining her power as a magical girl, and taking a stand to save Miyu!

Thanks to sniping from Kuro, Illya's group managed to slip away from Beatrice and retreat from the Ainsworth mansion for the time being. Then they try to regroup at the school building Bazett and Kuro and have been using as their base. However, Illya couldn't figure out a way to counter their Cards: Archer (Gilgamesh), and Berserker (God of Thunder, Thor), leaving her dejected. Seeing her like that, Kuro suddenly turns her twin swords at Illya and attacks?!

Bazett's barrier was supposed to prevent surprise attacks from the dolls, however Illya finds a little girl, Erica, sneaking into their school. For some reason Erica calls Illya "Onee-chan", and the two of them quickly hit it off. Meanwhile, a man claiming to be Erica's father appears. He seems kind at first glance, and while he came to pick up Erica, he's also...?!

The man who came to pick up Erica proclaims himself as Darius, head of the Ainsworths and Miyu's kidnapper. Using his great power Darius activates an ice-barrier Noble Phantasm. Even with Kuro's Caladbolg, their attempts to break the barrier barely scratch it while Darius delivers a shocking statement to Illya!

Illya has been kidnapped and taken to the dungeon of the Ainsworths' mansion. Erica wants to grant Miyu's wish to be with Illya, so she swaps Illya's mind into a stuffed bear. Thanks to her willpower and imagination Illya manages to gain the freedom to move, but when she starts searching the mansion for her body, Beatrice discovers her...

With Sapphire in hand, Illya transforms into a magical girl while still a stuffed bear. Her fierce battle with Rin and Luvia, whose minds have been replaced, leads them all to the bedroom occupied by Erica and Angelica. After regaining her original body, Illya continues to fight Angelica and learns the hidden truth about Miyu.

Sacrifice Miyu and save the world... The Ainsworths' true objective is to use Miyu, the Holy Grail, to save all mankind. The new turn of events sends Illya into confusion. Kuro rushes to her aid, immediately saying she values Miyu more than some parallel world. Meanwhile, with the fate of a world and Miyu hanging in the balance, Illya struggles to find her answer...

"I'll save both Miyu and the world!!" But for Illya to realize that wish of hers, she'll have to first rescue Miyu from the Ainsworths' clutches. While Illya is forced to face a fierce battle, Gil and Bazett appear out of hiding to overturn their disadvantages. At long last, Illya's reunion with Miyu draws close!

The battle heats up as Julian's magic comes undone and he threatens Miyu's friends with a horde of Heroic Spirits pouring out of a mysterious, black cube! Emiya Shirou, Miyu's older brother, rises to the occasion after his rescue, fighting alongside Kuro to break past Angelica and face Julian! But his charge is stopped by... someone new? And what does Gil realize during their battle?

With Shirou down, Illya and the others are completely cornered by the infinite horde of Heroic Spirits pouring out of Julian's dark cube. All seems lost when a mysterious sword appears before them! Seizing the new sword, Illya finally puts a stop to the spill, but Julian and Erica escape. Finally able to relax, everyone, including the abandoned Angelica proceeds to Shirou's home to recoup, where they see a whole new side of Miyu.