In the 21st century, the tomb of the legendary half-divine Sumerian King of Uruk, Gilgamesh, is discovered by archaeologists. When it becomes apparent that the tomb of Gilgamesh may in fact have supernatural properties, a huge research facility is built on top of it and many of the world’s brightest scientist flock to this "Heaven’s Gate" to advance mankind’s knowledge.

        A terrorist act destroys the facility and in the ensuing chaos, civilization itself is threatened during an event dubbed "Twin X". After Twin X, an unusual electromagnetic phenomenon, the Sheltering Sky, has surrounded the Earth. Disrupting many electrical reactions, the Sheltering Sky has seemingly brought progress on the planet to the halt.

        Years after Twin X, two siblings, Ensaki Kiyoko and Ensaki Tatsuya, find themselves protected from gangsters by mysterious young men with supernatural powers. These men are more than they appear, as they are dangerous creatures called Gilgamesh and allies of the terrorist who caused Twin X, a man who now has named himself after King Gilgamesh’s legendary best friend, Enkidu: the same man who also happens to be their father. A mysterious Countess and her three telekinetic wards seemingly oppose the Gilgamesh, and Kiyoko and Tatsuya soon find themselves drawn into a battle between factions they can barely understand, let alone trust.