The backdrop of Gilgamesh is the fight between two opposing forces. One of the forces is known as the Gilgamesh, lead by Terumichi Madoka (better known as Enkidu), and the other side is the Countess of Werdenberg and the three Orga-Superior children who live with her. In appearance, the Orga-Superior are indistinguishable from humans. However, they carry a special power known as "Dynamis" which allows them to use psychic energy and control objects using only their mind. The overarching theme of Gilgamesh is one of choosing sides.
The tomb of Gilgamesh in Uruk from the story 'The Epic of Gilgamesh' is discovered by a young genius-scientist named Terumichi Madoka, who is drawn to the energy called Dynamis, a word meaning 'power', resonating from the site. He reports his findings, and all of the world's best scientists gather there and a research facility called Heaven's Gate is built to do research on Gilgamesh himself. Their goal is to find out the factor in his genetic material which makes him a half-god, and eventually to find out the secret to eternal life. The scientists who work there clone themselves as embryos that would be used if something were to happen to the scientists.
When an unknown life form called Tear materializes in Delphys (a pit that seems to have no dimensions and that surrounds the tomb of Gilgamesh) and begins to contaminate embryos that surround it, the scientists stop all of the experiments. Dr. Madoka goes down to Delphys, breaches all of the guards around it and comes into direct contact with Tear, causing an immense explosion that blocks out the sky with a mirror-like layer. This is considered an act of terrorism, as after the explosion, computers and wireless communications stop working, and the planet falls into war and famine. The human population is nearly wiped out. This occurs on October 10, so the incident is called "Twin X" (after the Roman numeral symbol for the number 10).