The heroine of the story, Amu Hinamori, is a transfer student at Seiyo Elementary. At first glance, her classmates deem her "cool and spicy" and rumors speculate about her personal life. However, her real personality is that of a very shy girl who has trouble showing her true personality. One night, Amu wishes for the courage to show her "would-be" self, and the next morning finds three brightly colored eggs—red, blue, and green—in her bed. At first, she is alarmed, but realizes she must have really wished to change. These eggs hatch into three Guardian Characters: Ran, Miki, and Su. The Guardian Characters aid Amu in discovering who she truly is and help fulfill Amu's dreams. Amu's life becomes much more complex as she struggles to deal with her "would-be" selves and the Seiyo Elementary's Guardians, who recruit Amu to search for X Eggs and X Characters, the corrupted forms of peoples' dreams.

However, the Easter Company is extracting people's eggs in search of a special egg called the Embryo. The Embryo is believed to able to grant any wish to the one who possesses it. However, the process creates X Eggs and X Characters.

Amu's three Guardian Characters, Ran, Miki, and Su, aid her in her quest of self-discovery. Each Guardian Character represents an aspect of Amu's true self. Ran represents Amu's desire to be more honest and athletic, Miki represents Amu's desire to be more level headed and artistic, while Su represents Amu's desire to be more caring and improve her domestic skills. Moreover, the Character Guardians are more than mere mascots who help Amu learn about her true self. They can also perform a transformation where Amu's personality is replaced by an entirely different one.

However, Amu is not the only one with Guardian Characters. Each of the Guardians—Tadase Hotori, Nadeshiko Fujisaki, Kukai Soma, and Yaya Yuiki—have their own Guardian Characters. Amu also encounters Ikuto Tsukiyomi and Utau Hoshina, two siblings who also have Guardian Characters and are employed by the Easter Company to search for the Embryo.

However, the Easter Company is extracting people's eggs in search of a special egg called the Embryo. The Embryo is believed to able to grant any wish to the one who possesses it. However, the process creates X Eggs and X Characters. ♥♣♠♦