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

Kimihiro Watanuki is a young boy with a cursed gift. He has the ability to see evil spirits, and somehow they seem attracted to himself. One day he meets a mysterious woman who names herself Yuuko. She claims to have the means to end his torment, but she never works for free, and she wouldn’t help him until he works for her enough to pay for her services. Thus he starts to work in her shop and discovers that in that place, nothing is what it seems.