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.

God has abandoned the world. As a result, life cannot end nor can new life be born, and the "dead" walk restlessly among the living. Granting one last miracle before turning away forever, God created "gravekeepers," mystical beings capable of putting the dead to rest through a proper burial. Ai, a cheerful but naïve young girl, serves as her village's gravekeeper in place of her late mother. One day, a man known as Hampnie Hambart, who is supposedly Ai's father, arrives and kills all the people in her village. Having lost her village and with no plans for the future, Ai decides to accompany the mysterious man on his journey. As she travels the land, the young gravekeeper strives to fulfill her duties, granting peace to the dead and assisting the living, while at the same time learning more about the world that God left in this tragic state. [Written by MAL Rewrite]

Miya Tachibana, assuming her annoying brother Junichi will be unlucky in love and alone forever, decides to spy on him at school after hearing that some of her friends find him to be kind and caring. Through her spying, she learns that he gets along well with girls at school, which results in an even bigger misunderstanding, as Miya wrongfully assumes he likes men since he doesn't have a girlfriend. However, after she herself rejects a boy, Miya starts questioning how she views Junichi as she is reminded of Junichi's similar experience from two years earlier. [Written by MAL Rewrite]

The war on terror exploded, literally, the day Sarajevo was destroyed by a homemade nuclear device. The leading democracies transformed into total surveillance states, and the developing world has drowned under a wave of genocides. The mysterious American John Paul seems to be behind the collapse of the world system, and it's up to intelligence agent Clavis Shepherd to track John Paul across the wreckage of civilizations and to find the true heart of darkness—a genocidal organ.