The story follows Alice Seno, a 15-year-old girl forever shadowed by her older sister Mayura, who is good at everything she does. At school she is known as "Mayura's little sister" and is relentlessly tormented by the older girls who know that Alice is too weak to fight back.

Alice harbors a deep affection for Kyo Wakamiya, a handsome upperclassman who is on the archery team with Mayura. On the way to school one day, Alice rescues a white rabbit from the road despite the danger to herself, but gets rescued by Kyo and receives a bracelet with a single red stone. The rabbit she saves, however, is no ordinary rabbit. She reveals her true form to Alice and introduces herself as Nyozeka. Alice is told that she is destined to become a Lotis Master. The Lotis Masters use the power of words and communication to enter the Inner Heart of others. It is a powerful ability to be used carefully as Alice soon finds out.

Using the power of the Lotis Words, which reveal themselves to be in the form of runes, Alice accidentally makes her older sister disappear during a dispute over Kyo, whom Mayura had begun dating. Alice then must use the Lotis Words to try and bring her sister back from the dark. She is joined by Kyo who proves to have the Lotis powers as well, and by Frey, another Lotis master who had trained with the masters and arrives with the intention to marry Alice. Unfortunately, Mayura has been taken by the power of the Maram Words, the dark reflection of the Lotis Words. Their only hope lies in Alice and Kyo becoming the legendary Neo-Masters to discover the lost word bonding both Maram and Lotis.