Illya has been chosen by the Kaleidostick Ruby to become the new magical girl.

A challenger appears, just when Illya is having trouble collecting the Rider card under Rin's instructions.

A mysterious transfer student, Miyu Edelfelt, has joined Illya's class. Is she friend or rival?

Illya and her friends have been defeated by Caster. They must figure out how to improve their teamwork in order to win the rematch.

There is no time to celebrate their hard-won victory, as Saber card suddenly appears to strike down Rin and Luvia. Faced with their strongest opponent yet, which option will Illya and Miyu choose?

Illya calls upon the power of the Archer card to defeat Saber.

Illya stays home to recover from a fever, but gets into some hijinks with Miyu. That night they attempt to capture the Assassin card.

Suffering from shell shock, Illya tells Rin she wants to resign from being a magical girl. But fate has something different in store for her.

Miyu attempts to capture the last card by herself using Saber's power.

Illya and Miyu must combine their strength in order to defeat Berserker whose Noble Phantasm allows him instant resurrections.

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.

As Illya and her friends prepare for a trip to the beach, Mimi stumbles across Illya and Kuro doing their 'mana transfer'. Afterwards, Miyu comes over to Illya's house for a sleepover, where she acts bashful around Shirou.

Illya and her friends arrive at the beach alongside Shirou and his friend Issei Ryuudou. Whilst enjoying the beach, Miyu tells about how she has a brother, who Shirou resembles, before the girls come across Bazett, who is working part-time jobs to pay off her debts. Later, as everyone has a party to celebrate Illya, Miyu, and Kuro's birthdays, the celebrations are interrupted by some noisy construction from Rin and Luvia, who are attempting to dig for the eighth card, with Illya soon finding herself in the middle of an outrageous feud. Things become more troublesome when Ruby tries to inject Shirou with a love potion, though Sapphie soon sorts things out by erasing everyone's memories.

Plagued by thoughts of lewdness surrounding Illya and Kuro, Mimi starts putting her thoughts down into story, which soon turns into a gender-swapped boy's love story. This soon catches the attention of her classmate Suzuka Kurihara and her sister, who decide to use her story for a yaoi doujin. Concerned about Mimi's gradual transformation into a fujoshi, Suzuka asks Illya, Miyu, and Kuro for their help. Despite not being fond of Mimi's fascination with BL, Illya learns that it doesn't mean they can't still be friends.

Illya receives tickets to a theme park from Luvia and decides to go with her friends. When they lose track of Irisviel, who gets swept into a special event, they come across Caren, who agrees to be their substitute guardian. Later, Illya discovers the charm on her bracelet has gone missing, so Miyu decides to help her search for it. Taking some advice from Caren, Miyu manages to deduce the charm's location and find it before closing time. Afterwards, Kuro becomes curious about the relationship between Irisviel and Caren.

The girls attend the local summer festival, where Illya shows Miyu how to enjoy herself. Later, Rin and Luvia get into mischief in front of Shiro, while Illya uses her transformation to escape a wardrobe malfunction. Meanwhile, Kuro becomes aware that Miyu is hiding some kind of secret from Illya.

Having completed reconstruction of her mansion, Luvia invites everyone over for a house party, after which the girls discuss their plan to obtain the eighth card. As the girls prepare for what could be their final mission, Kuro questions Irisviel over how the cards are related to the Holy Grail War, which involved only seven classes. Ruling out the possibility of Irisviel being involved, Kuro suggests that they question Miyu, but Illya feels it is best to focus on the task at hand and find the answer themselves.

The girls are joined by Bazett, who reveals she had dispelled the curse of shared pain a while back, before entering the Mirror World, where they are confronted by the eighth card, shrouded by a black mist. Following their plan, Luvia restrains the enemy while Rin provides a mean to enhance Illya and Miyu's attack, providing an opening for Kuro to attack. However, the enemy manages to block it with a shield and counterattacks, forcing the girls to retreat while Bazett charges in, only to get stabbed by multiple swords wielded by the enemy. As Bazett fights using the Berserker's power, Illya and Kuro stay behind to give her a chance to strike, but are still unable to defeat it. Barely managing to escape, Bazett informs the others that the enemy possesses a second Archer card, before it suddenly appears in the real world.

Luvia collapses the ceiling onto the enemy so that everyone can escape, but it transforms itself into a craft that starts heading towards the city. Just then, the girls are approached by Caren, revealed to be an observer for the Holy Church, who had placed a bound field around the city to keep anyone from seeing anything, giving the girls an opportunity to rest. As Caren theorises that the creature is targeting the Holy Grail, with Kuro deducing it relates to a different Holy Grail War entirely, the enemy starts heading towards Mt. Enzou, where it uncovers a magic circle. While trying to push them out of it, Illya pushes out a human boy that was inside it.

As Caren experiences backflash from her observation spell, the boy, revealed to be the Heroic Spirit of the eighth card, reveals that Miyu is a princess from a parallel world who was born as a complete version of the Holy Grail. Feeling she can't escape her fate, Miyu gives Sapphire to Illya before being pulled into the vortex, completing the Heroic Spirit's ultimate form. Learning that Miyu is still alive inside the demon's body, Kuro and Bazett hold off the demon while Illya, gathering her resolve to rescue her friend, combines Ruby and Sapphire's power to unleash a powerful new transformation.

Using her new power, which puts her own body at risk, Illya fights back against the demon while Kuro and the others provide support. As the demon brings out his strongest sword, Ea, Illya uses her full power to defeat it and finally rescue Miyu. Following the battle, Illya and her friends get together to finish their summer homework, with Miyu more than happy to help. Meanwhile, Irisviel and Caren discover the crater has disappeared into a parallel world, where the eighth card is recovered by a mysterious pair.

The girls learn that the crater created in the mountain during their previous battle has mysteriously disappeared. While investigating the scene, they are suddenly confronted by two new adversaries who overwhelm them and kidnap Miyu. As Illya tries to chase after her, she finds herself in parallel world covered in snow, where she meets a peculiar girl known only as Tanaka. Despite seemingly having no other memories, Tanaka is somehow able to tell Illya that Miyu has been kidnapped by the Ainsworth Family.

Illya and Tanaka are attacked by one of Miyu's kidnappers, Beatrice Flowerchild, before she is suddenly called away. As Tanaka explains that the only thing she remembers is her duty to eliminate the Ainsworth family, she and Illya come across a ramen shop, where the owner explains that a gas explosion caused the crater. When they are suddenly faced with a hefty bill, they are bailed out by the Heroic Spirit Illya previously faced, Gilgamesh, who helps lead them to the Ainsworth's castle in the center of the crater. Making their way inside the castle, they come across a prison cell containing Miyu's older brother, who urges them to save Miyu. Just then, they are confronted by the other of Miyu's kidnappers, Angelica.

Gilgamesh steps up to face against Angelica while Illya and Tanaka go off in search for Miyu, only to come up against Beatrice again. As Tanaka takes on brutal attacks from Beatrice, Illya manages to find Ruby among a pile of weapons, transforming once again and installing the Caster card to fight against Beatrice's Berserker. After Tanaka takes on a full blast from Beatrice, still managing to survive, Gilgamesh helps her and Illya make a retreat. Just as Beatrice and Angelica catch up to them, they are called off by the head of the Ainsworth family, Darius Ainsworth, while Kuro and Bazett also arrive in the parallel world.

Kuro brings Illya and the others to the school, which she and Bazett had been using as a base. Kuro then explains their situation while Bazett gives Illya the Saber, Rider, and Lancer cards. As Gilgamesh explains to Bazett what the cards are, Kuro, notices Illya feeling sorry for herself, confronts her in a battle, forcing her to use the cards she received from Bazett to defend herself. During the battle, Kuro informs Illya that her fears of being in an unknown world are the same feelings Miyu kept to herself all the while. Winning the battle with the Saber card, Illya comes to understand what Kuro was teaching her.

Illya helps out a girl named Erica after she gets stuck on the school's walls and wets herself. As the girls take a bath together, they learn that Tanaka had lost her memories just before meeting Illya. Afterwards, as Sapphire manages to get in contact with Ruby, Erica is picked up by her father, who turns out to be Darius himself.

Darius traps Illya inside an ice barrier Noble Phantasm which slowly cuts off her oxygen supply. Tanaka manages to break through the barrier, allowing the others to come to Illya's aid, but they are all helpless to fight against Darius. After taking an interest in Tanaka's abilities, Darius takes his leave, with Erica leaving some disturbing words for Illya. As Illya and the others try to figure out their next move, Darius performs a painful ritual with Miyu. The next day, Kuro discovers that Illya has disappeared, leaving her Class Cards behind.

Illya wakes up to find she has been kidnapped by the Ainsworths who, after failing to brainwash her, transferred her mind into a stuffed animal, placing a fake personality in her original body. Managing to take control of her new plushy body, Illya tries to chase after her original body but is caught by Beatrice, who brings her to her room. Before Beatrice can rip her to shreds, Illya is saved by the arrival of Rin and Luvia, only to discover they have also been brainwashed into becoming maids. Escaping to the loft, Illya manages to find Sapphire, who gives her the power to transform.

Learning that injuring the possessed bodies will bring their original minds back, Illya, still powerless despite transforming, tries to fight against the possessed Rin and Luvia, who utilise nameless Noble Phantasms to fight against her. As they end up crashing into Erica's room, where Angelica finds them, Illya manages to use split-second timing to return to her original body. As Angelica uses displacement magic to overwhelm Illya, she reveals that the Ainsworths are trying to save their world, which is slowly dying, by using Miyu as the Holy Grail.

Angelica further explains the situation that because the world's decreasing mana is killing off lifeforms, the Ainsworths intend to use the Holy Grail to change humanity into a species that can survive in this new environment. Forced to use the Assassin Card to escape, Illya, conflicted over choosing between Miyu and humanity, is rescued by Kuro, who states her determination to save Miyu regardless of the situation. As Darius forces Miyu to watch everyone's battle, Illya comes to her own decision, stating her determination to save both Miyu and the world without sacrificing either.

As Gilgamesh and Bazett sneak up from behind, managing to bring Rin and Luvia back to their original bodies, Illya pushes ahead to confront Darius, using a card she received from Kuro to hit him with a dagger planned to cut off his magic, reuniting with Miyu in the process. However, emerging from Darius' body is his son, Julian, who reveals a large black cube in the sky and uses its dark power to consume Erica and create an army of Heroic Spirits. Just as the army seemingly overwhelms them, they are saved by the arrival of Miyu's brother, who bears a strong resemblance to Shirou.

Putting his own body at risk to use his Trace On ability to create weapons, Miyu's brother is aided by Kuro as he battles Angelica while the others fight off the Heroic Spirits. After Kuro manages to use teleportation to defeat Angelica, Miyu's brother goes after Julian but is heavily injured by a mysterious and deranged woman. As Miyu uses the Archer card to confront her, she becomes possessed by it until Gilgamesh retrieves it from her body. As Julian dispels the woman, Illya brings out her full power in an all-out attack.

As Illya's attack fails to stop the regenerating army, Tanaka throws a mysterious sword into the middle of the fray, allowing Illya to damage the black cube and dispel the muck causing the army to grow. As Julian escapes with Erica and Beatrice, Bazett manages to retrieve a gem allowing Rin to properly heal Miyu's brother. After everyone, including Angelica, returns to Miyu's home, Illya and Kuro discover the sword she used was actually Tanaka's arm. While Julian prepares his vengeance, Miyu and her brother tell the others about what happened to them.