Soul Hackers 2 takes place in the 21st Century and is set during a war between the Yagaratsu and the Phantom Society, two opposing factions of Devil Summoners. The story follows two supernatural "Aion" beings named Ringo and Figue, who descend into the human world from their birthplace in the data stream of information, in order to avert a cataclysmic event that they predict will doom humanity

Amidst the glimmer of neon lights, technological advancement causes humans to be consumed by commercial convenience. In the shadows, a war between the Yatagarasu and the Phantom Society is brewing, Devil Summoners who harness the otherworldly powers of “Demons”. Existing in the secret sea of humanity’s data, a digital hivemind has evolved into sentience: Aion. Observing humankind from afar, Aion calculates that a world-ending disaster is imminent and creates two agents to combat against it: Ringo and Figue. Together, these agents of Aion must investigate and prevent a butterfly effect that will lead to the end of the world.