The heroine of the story, Amu Hinamori, is a student at Seiyo Elementary. At first glance, her classmates refer to her as "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 as the Joker to search for X Eggs and X Characters, the corrupted forms of peoples' dreams.

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

Continues on "Shugo Chara! Encore!"