Season 2

With the ley lines failing to recover despite the cards being retrieved, Rin and Luvia bring Illya and Miyu with them to help seal the lines. However, something goes wrong, leading Illya to become split into two separate people.

Illya finds herself targeted by her dark clone, Kuro Illya, whose creation has resulted in Illya's power becoming weaker. Rin and the others attempt to lure Kuro into a trap, but her ability to read everyone's moves leaves them at a disadvantage. However, Illya manages to draw Kuro into a bog, allowing her to be captured.

After failing to get any information from Kuro, Rin places a seal on her that would cause her pain if anything happens to Illya. When Kuro escapes, Illya has to take drastic measures to keep her from making moves on Shirou. The next day, Kuro causes more problems for Illya when she starts randomly kissing other girls at school to replenish mana. When the two are spotted together by her classmates, Kuro decides to pose as Illya's cousin.

Kuro transfers into Illya's class, much to Illya's dismay, and is immediately thrust into a dodgeball match against the classmates she kissed the other day. Feeling her school life is at risk, Illya steps in to challenge Kuro one-on-one, with both sides bringing out their full magical power. Kuro lands a critical hit on Illya's face, but due to their shared pain they both pass out, ending the match in a draw. Whilst recovering, Kuro suspects the school nurse knows more about her existence than she lets on. As Shirou comes to pick up Illya, Miyu is a little perturbed by Kuro's words that she shouldn't stay too close to Illya, lest she find out things she has been keeping secret.

After Illya inadvertently blows up her house's bathroom wall, her family comes over to Luvia's house to use her bathroom, where Kuro causes more trouble for Illya. Later, as Rin and Luvia ask Illya about how she used the Archer Card in the manner she did, Illya's statement of wanting to return to a normal life angers Kuro, who reveals she herself possesses the Archer Card and escapes. The next day, Miyu is summoned by Kuro, who claims Illya's wish of a normal life excludes Miyu and the other people she had met as well too. However, Miyu has faith in her friendship with Illya and uses the Saber Card to stand up against Kuro.

Miyu and Kuro have an intense battle before Illya arrives to try and stop them, apologising for the words she said before. When Irisviel suddenly arrives to pick Illya up, Kuro tries to attack her, but she stops her with her own magic. Irisviel reveals Kuro was sealed away so that Illya can become the Holy Grail, with Kuro becoming upset when she learns the Holy Grail War no longer takes place, feeling she has no place to belong. She ends up overusing her mana and starts to disappear, but Illya gives her some of her own mana so that she can last longer. Told by Illya to make her own wish come true, Kuro wishes to have a family, allowing her to come back into existence as a proper member of Illya's family.

Illya ends up competing in a baking contest against Kuro, winding up at a disadvantage due to one of her teammates adding bizarre ingredients. The next day, Illya tries to learn how to be regarded by Kuro as a "big sister", with not much success. Everyone also find out that Illya, Kuro and Miyu have the same birthday of July 20th. Later, Kuro states how she is relying on Illya to keep supplying her with mana.

Irisviel has Rin and Luvia sneak her into Illya's school to observe her during classes, later asking them to leave Illya and Kuro to their normal lives. Later that day, as Rin observes a change in the ley lines and Miyu is sent on an errand, a mysterious woman named Bazett Fraga McRemitz appears before Luvia, demanding she hand over the Class Cards. As Luvia and her butler, Auguste, battle against Bazett, Rin tries to find the opportunity to launch a sneak attack, but both their attacks fail, as Bazett prepares to make a move against Illya and Kuro.

Bazett, who was previously responsible for collecting the Class Cards, launches a fierce attack against Illya and Kuro in an attempt to take their cards, completely overwhelming them. Just as they are cornered, Miyu arrives and uses the power of the Rider card Illya managed to protect to fight back against Bazett.

Bazett uses her weapon, Fragarach, to counter Miyu's strongest move and take her card, soon setting her sights on Kuro. However, working together with Kuro and Ruby, Illya manages to activate a seal that Rin left behind, allegedly giving her the same curse as Kuro and leaving her unable to harm Illya. Rin also reveals the existence of an eighth card, convincing Bazett to form a truce and leave Illya with half of the cards. As the girls resume their everyday lives and look forward to their trip to the beach, the mysterious eighth card lies in slumber.