While being pursued by tax collectors, siblings Tatsuya and Kiyoko Madoka find shelter with the Gilgamesh, a group of strange youths with psychic powers.

The Gilgamesh, revealing themselves as horrible monsters, do battle with the Orga-Superior--three children under the care of a woman called the Countess. Tatsuya and Kiyoko are soon taken into the Countess's custody.

The Madoka siblings acquaint themselves with the Countess, who wants them to fight against the Gilgamesh. Another battle begins, and though the siblings want to get away, the Countess has other plans.

Now legally owned by the Countess, Tatsuya and Kiyoko are taken to their new home, the Hotel Providence. Investigation begins on the wing of antimatter cut from the Gilgamesh Uno in the previous battle.

Tatsuya becomes fascinated with Dynamis, the energy force central to the Orga-Superior's psychic powers, as well as his own emerging Dynamis abilities. The Gilgamesh continue to pursue the siblings.

Final Showdown of the Gilgamesh.