A year has passed since the Star Force returned to save the Earth but another danger now approaches from deep space. A gigantic White Comet hurtles toward our galaxy, obliterating everything in its path. But it is no ordinary comet—it is the deadly Comet Empire, conqueror of worlds... and Earth is the next target! Against orders, the Star Force blasts off to investigate, but even if they can get past the flagship Andromeda, they don't yet know the true nature of their new enemy! (Source: AniDB)

The Great Kanto Desert, a sweltering wasteland of nothing but ruins and sand, is all that remains of post-apocalyptic Japan. The once fair population has been left to cling to the inhospitable dunes for survival. At least, that is the case for normal people. For those who have spent a little too long in the Kanto sun, the desert offers a wondrous opportunity to make a name for themselves. One such person is the masked handyman "Sunabouzu," or Desert Punk, who has forged a legendary reputation for always finishing his jobs, no matter the nature or cost. Cunning and ruthless, he has become a force of crude destruction to the other desert people. However, the "Vixen of the Desert," Junko Asagiri, discovers that Sunabouzu is not without his weaknesses—he is easily swayed by his insatiable lust for large-breasted desert babes. Following their chaotic adventures through the Kanto Desert, Sunabouzu features a bizarre cast of personalities who entertain themselves with senseless violence and perversion in a world long destroyed by their forefathers. And just like them, they have not learned a damn thing. [Written by MAL Rewrite]

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.

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.