At the close of the millenium, the battle for humanity's future is staged. Kamui Shirou's destiny has been decided as he returns to Tokyo to face his ultimate challenge. The Dragons of Heaven, defenders of humanity, stand ready to protect the world from the Dragons of Earth, the seven angels of legend who embrace the eradication of mankind to bring about the planet's purification. Now Kamui must decide which side to fight for although he finds the idea utterly unappealing. It isn't until realizing that his two childhood friends, Fuma and Kotori Monou, are in grave peril that Kamui decides to step into his fated position in the climatic struggle of the Year of Destiny: 1999.

4000 years have passed since humanity abandoned Earth. Forced to fight an alien form of life, Gnosis, mankind developed KOS-MOS - a battle android with amazing capabilities. When a ship carrying android is being attacked, KOS-MOS gets activated and save its creator, Shion Uzuki. But KOS-MOS doesn't want to listed her orders and executes some unknown plan. After their ship destroyed Shion and her companions find themselves thrust into the middle of a battle with Gnosis, U-TIC Organization and their own superiors. Battle with no clear sides...