Kaoru Mikogami, an elite assassin for the Imperial Intelligence, is paired with Alice, a combat android developed by the US Army. While targeting an AI researcher, Kaoru discovers the mission is a lethal trap orchestrated by the mysterious Massy Spector. Amidst the chaos of a staged terrorist attack and a ticking bomb, Kaoru and Alice begin an unlikely partnership in a world scarred by the enigmatic XINN phenomenon.
As Mikogami investigates "Ninth Heaven," a cyber drug linked to the sinister "Shadows" and MJP technology, his sister Kaoru is kidnapped and subjected to horrific torture. Though Mikogami and Alice rescue her, Kaoru is left physically and mentally scarred. Amidst the chaos, it is revealed that Massy's consciousness has migrated into Alice's brain, triggering system instabilities and unveiling a dark plot by Digital Demand to engineer a digital deity.
After an intimate encounter between Kaoru and Alice triggers the awakening of Mayumi, Kaoru's long-lost sweetheart, he discovers a sinister plot to create "Xinn," a digital god born from the global network. As Mayumi's consciousness merges with Xinn to dominate humanity, Alice's remaining personality fights for control, ultimately pleading with Kaoru to kill her to stop the entity. Following a tragic sacrifice and the destruction of Xinn, Kaoru is left to mourn the loss of both women while hoping their spirits still linger within the virtual realm.