Amu Hinamori is a student at Seiyo Elementary, where she has a reputation for being "cool and spicy"; however, her real personality is that of an extremely shy and easily intimidated girl. One night Amu makes a wish that she would have the courage to be reborn as her "would-be" self. The next morning Amu finds three brightly colored eggs—red, blue, and green—in her bed. Each egg eventually hatches into a Guardian Character: Ran, Miki, and Su. Guardian Characters are angel-like beings that aid a person into becoming their "would-be" selves and fulfill the person's dreams. The Guardian Characters accomplish this by giving encouragement and advice, but they can also temporarily change a person's personality and abilities. With the Guardian Characters, Amu's life becomes much more complex as she now struggles to deal with her new personalities and the Seiyo Elementary Guardians—a student council group where each member has their own Guardian Character—who recruits Amu to search for and seal the X eggs and X Characters, corrupted forms of people's dreams.

Amu meets a super-peppy transfer student at Seiyo Academy Elementary School named Hiiragi Rikka at school one day. Not only can she see Guardian Characters, but it seems she has some other, mysterious powers as well. When she sees the work that Amu and the other Guardians do at school, she's awestruck. Each 24-25 minute episode consists of a series of variety show style shorts (including Shugo Chara! Pucchi Puchi) totaling approx. 9-10 minutes, followed by the main 11-12 minute animation titled Shugo Chara!!! Dokki Doki which is the actual continuation of season 2 and comes with it's own opening animation. The remaining time is occupied by live action padding between each section and capped off with the opening/ending themes at the beginning and end of the episode. (Source: AniDB)

Now Utau has left Easter and restarted her singing career, while Ikuto still remains at Easter. To replace Utau Easter hires a new character, Lulu. Lulu has the power to create question mark eggs, instead of x-eggs. Throughout this season we start to see all the love interests more so then in the first season. Tadase and Amu seem to be a couple now, but they have their problem, especially when Amu starts hiding Ikuto in her room. She lies to Tadase, her family and all the Guardians about it, which in the end causes more problems then she expected. Easter also has a new plan to control Ikuto. Using his violin Easter controls Ikuto so that he transforms into Death Rebel. The sound of his violin turns all the heart eggs with in distance into x-eggs. With a large amount of x-eggs gathered, the embryo will soon turn up. (Source: ANN) Episode numbers continue as 52, 53, 54, etc.

In the kingdom of Xoana, Lina Inverse and Gourry Gabriev unexpectedly come across their old companions, Zelgadis Graywords and Princess Ameilia Wil Tesla Saillune. Upon their reunion, the friends end up easily foiling the King of Xoana and his daughter's dastardly plans of world conquest. Soon after, it is revealed that Zelgadis is in search of the world's most valuable magical tome, the Claire Bible, hoping to discover a method to recover his human body among the many secrets sheltered within it. Despite his protests, the rest of the group decides to join in the quest after hearing of his mission. However, just when they were wondering where to start looking for the legendary book, they stumble upon a mysterious priest by the name of Xellos, who claims that he may be of some help in their pursuit. [Written by MAL Rewrite]