The story of Child of Eden is revealed through the game's introduction. It focuses on a girl named Lumi who was the first human to be born in space, on 11 September 2019 aboard the International Space Station. Throughout her life, Lumi dreamt of visiting Earth, conveying her feelings into song which she sent down to the people of the planet. When she died her body was preserved and her memories and data were recorded and archived. The story moves to humanity's advancement in space exploration, and the creation of a universal wide internet system called Eden. Eden is described as a fountain from which all knowledge flows, to those who have never set foot on Earth, containing all of human history and knowledge. By the 23rd century scientists attempt to use Lumi's preserved data to create a living persona with Eden itself, in an experiment called Project Lumi. As her recompiled persona emerges and awakens into Eden, she is attacked and trapped by an unknown computer virus.

The game is set in futuristic computer "supernetwork" called Project-K where much of the data flow is controlled by an AI named Eden. Eden has become overwhelmed with the amount of knowledge gathered on the network, causing her to doubt her existence and enter a shutdown sequence, which would create catastrophic problems everywhere should she be able to complete this.