Illyasviel von Einzbern is an ordinary elementary school student who becomes a magical girl when the magical Kaleidostick Ruby deems her a more suitable master than the sorceress, Rin Tohsaka. Rin, who had been tasked by the wizard Zelretch to collect the seven Class Cards containing the spirits of Heroic Spirits from legend, finds that she is unable to change Ruby's mind and must supervise Illya in completing the task of collecting the Class Cards. During Illya's adventures, she receives a friend and rival in a girl named Miyu, the contracted master of the Kaleidostick Sapphire, which similarly abandoned its original master and Rin's rival, Luvia Edelfelt.
After a series of battles, Illya and Miyu were able to collect all Cards and became good friends, while Rin and Luvia remained in Japan by the order of Zelretch. However, the appearance of Kuro, a dark-skinned girl with a striking resemblance to Illya, soon complicates their lives as she attempts to eliminate Illya. Their battle is interrupted by the arrival of Illya's mother, Irisviel, who reveals that Kuro was originally intended to be the Holy Grail in the Holy Grail War, but after the war was prevented Kuro was sealed away so Illya could live a normal life. Illya supplies Kuro with the mana needed to sustain her physical form, and accepts her into the Einzbern family.
Shortly afterwards, the group is attacked by Bazett Fraga McRemitz, who was previously responsible for obtaining the Class Cards. A truce is forced when Rin reveals the existence of an eighth Class Card. The group confronts the eighth Class Card, Gilgamesh, who reveals that Miyu hails from a parallel world where she was born as a Holy Grail, before absorbing her. Illya combines the Kaleidostick Ruby and Sapphire to become Kaleido Liner Zwei, giving her the power to defeat Gilgamesh and save Miyu.
This victory is short-lived, as Miyu is kidnapped by the Ainsworth family and whisked away into the parallel world. Illya and her friends enter the parallel world and teams up with Tanaka, an amnesiac girl whose goal is to defeat the Ainsworths; Gilgamesh, who wishes to take back his Class Card from the Ainsworths following his defeat by Illya; and a parallel Shirou Emiya, Miyu's older brother who is imprisoned by the Ainsworths. The Ainsworths reveal that they intend to use Miyu as the Holy Grail to save their dying world, but Illya swears that she will find a way to save the parallel world without sacrificing Miyu. Following a confrontation, the Ainsworths escape and Gilgamesh leaves the group after reclaiming his Class Card, while Angelica Ainsworth reluctantly joins the group after being left to die by her family and Miyu and Shirou are liberated.