The anime starts with the adventures of twelve-year-old junior high school student Hibari Hanakoganei living in Tokyo in the year 2010, who, like any girl, aspires to have a mobile pet of her own, called a “Pata-Pi.” During this time, PataPies are trendy and there is a nationwide craze in owning one. Simply buy one, upgrade it with pre-set or custom parts, and show it off to friends and relatives! However, Hibari has no money to buy one and can only admire her best friend, Suzume, as she flamboyantly praises her PataPi, Francesca.
Then one evening, as she is walking home, she sees a hill upon which a person is standing beside a tree at the peak and recognises it as the prince (Crane) who has been appearing in her dreams. She runs towards him but he disappears. Then a glowing sphere descends from the sky and lands on her palms. It materialises into a PataPi and she hugs it with all her heart. Thus the adventure of Hibari and Densuke the PataPi begins.
However, she is under the watchful eye of a certain shadowy character and is ambushed when she walks home from school. Attacked by strange creatures called Homunculus and confronted by a masked woman (Jun), Hibari finds out that they are after Densuke and strives to protect him. When all fails, Jun calls out a more powerful creature called Cerberus to harm Hibari. Out of extreme sympathy for Densuke, Hibari cries out and suddenly a light descends on Densuke. In moments, he transforms into a woman in an armour suit (Aphrodite), who defeats Cerberus and chases Jun away. Unknown to Hibari, a masked man in black (Takashi a.k.a. Shooting Star) stands at the top of a building, observing every moment of what happened.
The next few episodes focus on unlocking the Diva within the other PataPies, notably Suzume’s Francesca and Tsugumi’s Tetsuro, with some subtle intervention by Takashi. It also shows how the three girls get along (with disagreements sometimes) and form the Cyber Team in Akihabara, aimed at stopping masked women and their Homunculus from terrorising the city of Akihabara.
As the series carry on, a bit of the plot is revealed (with the principal Washu commenting on hazy stuff at the end of every episode) and the introduction of Kamome and Tsubame (who becomes the unknown enemy to the four girls until much later when she finally helps them). It is also revealed that Washuu is the founder of a Celtic organisation called Rosenkreuz (Rose Cross in German) and he himself is Christian Rosenkreuz, hiding under the name of Washu Ryuugasaki to carry out his agenda. He once worked for the famous alchemist Paracelsus and collaborated with a French man, Cigogne Raspailles, and a young American man, Crane Bahnsteik to invent a device that can grant immortality (Divas). However, due to their secrecy, none of their inventions is revealed to the world. After Crane discovers that inventions made by the world lead to World Wars and the implications of Divas falling into the hands of warmongers, he finally ran off to space in his invented space rocket, together with all the plans on the immortality project.
Later on, it is revealed that the transformation of PataPies into Divas is not one-sided: the owner of the PataPi can fuse with the Diva to form a complete Diva. This is only possible for those who are the chosen Anima Mundi and possess a pure and undefiled heart. Throughout the series, only Hibari and Tsubame managed to fuse with their Divas, although in the movie, all five girls eventually managed to do so. The fact that Takashi is a clone of Crane, and used by Washu like a puppet to awaken the sleeping Divas in space (kept in Crane’s space fortress the Primum Mobile), causes Takashi to rebel and find his identity in the world, with the three women Jun, Miyama and Hatoko joining him.
Towards the end of the series, Kamome’s grandfather, Shimabukuro Sengakuji, reveals everything he knows about Rosenkreuz (he once worked for Rosenkreuz), the concept of Divas, which are artificial forms powered by neutrinos, and the principal Washu who is the mastermind behind the events. Soon after, Washu discards his pseudo-identity, reverting to the original Christian Rosenkreuz, and changes the school into a large altar to welcome the descent of the Primum Mobile. He finds out that Crane was the one controlling the events that happened and dies soon after of old age. Then Crane issues an ultimatum to Japan that he seeks the Anima Mundi and will threaten to destroy the country and the world if it is not met. Finally, at the end, the girls rebel and the Divas sacrifice themselves in place of the girls.