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.

It's been several years and Kyosuke Kasuga is now 19. A mysterious phone call warns him of oncoming cars but he doesn't listen. Ironically, he gets hit by a car and because of his telepathic abilities, gets sent three years into the future. His 22 year old future self is now a photographer who is lost in Bosnia and believed to be dead. Kyosuke must find his 22 year old future self and restore himself, the 19 year old, to his correct time. Along the way he reunites with Hikaru who is now a professional and famous dancer. Madoka is also there, distraught over both Kyosuke, the 22 year old, going missing in Bosnia and Kyosuke, the 19 year old, getting hit by a car.