The story revolves around the lead of the story, Kirihara Aruto. It begins one night when Aruto is awake writing his own copy of The Endless Alice. Suddenly he sees a girl leaping through the night sky. Believing her to be the Alice he writes about, he leaves his house and follows her to a library.

He sees her fighting with another girl, who is defeated. The former then steals the latter's story and disappears. The next day, she reveals herself as Arisugawa Arisu, the female lead of the story. She then explains that she is an Alice User, capable of transforming into a kemonomimi bunny girl that uses a key in fights against other Alice Users. The keys are used to unlock the stories in other Alice Users's hearts. She explains that if a girl loses her story that she can no longer be an Alice User; the overall goal of an Alice User is to defeat all others and finish the Endless Alice. The one who does so will be granted a wish.

Later, Kirihara Kiriha, Aruto's little sister is introduced. Kiriha reveals herself as an Alice User and proceeds to fight Arisu. Aruto breaks up the fight and the two make peace. The trio agrees to help each other finish Endless Alice. The rest of the series follows their adventures together.