The world is being attacked by the mysterious "Victims" — giant space monsters sent to destroy Zion and all its inhabitants. Zion's only defense are the five Goddesses — sentient mechas, each bonded to her own pilot and repairer. With a high pilot turnover, it's up to the Goddess Academy (GOA) to train young candidates with gifted abilities (called EX) to one day become a pilot of a Goddess. Candidate #88- Zero has just joined the GOA and deep, dark mysteries and secrets soon unfold between Zero, the pilots & candidates, and the Goddess Ingrid as the Victims press their attack.

An ancient legend, a love that transcends time, and vengeance so bittersweet . . . An ancient legend has devastating and unfathomable consequences on 16-year old Aya Mikago. Her world turned upside down, Aya sets out on a journey to discover the truth about herself and the disturbing history of her family line.

In the future, personal computers have developped into "Persocons", mobile computers that look like human beings. Hideki Motosuwa, a prep school student, desperately wants to buy a Persocon but cannot afford to. One day he finds a Persocon that has been thrown away and decides to keep it. When he turns on the Persocon, all she can say is "Chii" so he decides to name her that. After a while it starts to become apparent that Chii is more than an average Persocon. Having much better performance, it seems that Chii might be a "Chobit", a type of advanced Persocon rumoured to have independent thought.