Aruto Kirihara, a high school student, possesses a deep obsession with the Alice stories by the enigmatic author L. Takion. He channels this passion into actively writing his own fanfiction sequel to the books. His ordinary existence shifts dramatically when he witnesses Arisu Arisugawa—a girl mirroring his imagined Alice—battling another girl in a nighttime library encounter. This event pulls him into the hidden world of the Seekers of Alice.

Aruto lives with his younger sister, Kiraha Kirihara, whose feelings for him extend beyond typical sibling affection into romantic territory. Kiraha frequently seeks his attention and displays jealousy toward other girls, particularly Arisu. Another classmate, Kisa Misaki, is often misunderstood as harboring feelings for Aruto, while her true affections are actually directed at Kiraha.

A traumatic childhood fire orphaned Aruto, leaving his Alice books as his sole meaningful possessions. This event fuels his emotional vulnerability and protective instincts. Though lacking combat abilities, Aruto holds a unique power: he can enter the Wonderland Space—the extradimensional battlefield for Alice Users—without transforming like the female participants. His primary ability allows him to transcribe and copy the "hidden stories" locked within the hearts of the Seekers of Alice. He typically returns these deeply personal stories to their owners, believing they should not be kept by others.

Aruto's creative power proves exceptionally strong, bordering on reality-warping. This ability manifests when he unconsciously wills Arisu Arisugawa into existence as a physical embodiment of his idealized Alice. This act replaces his sister in his emotional world due to his inability to reciprocate her romantic feelings, highlighting his need for an uncomplicated connection to the Alice narrative while complicating his relationships.

Throughout the story, Aruto evolves from a passive observer into an active participant. He aids Arisu and Kiraha in their battles against other Seekers, opposing figures like Akane Akatsuki—who seeks to destroy Alice-related stories—and the mysterious author figure Alternite L. Takion. Takion manipulates the Seekers into collecting stories to complete the mythical "Eternal Alice" grimoire, rumored to grant wishes. Aruto confronts Takion in the climax, rejecting the author's desire to use the compiled stories for personal gain and advocating instead for the preservation of each individual's narrative.