In the panic surrounding a worldwide pandemic which kills 15 percent of the population and cripples many more, a secret organization, the Propater, topples the UN and seizes control of much of the world. A boy and a girl, raised in an abandoned virology research center, immune to the virus, are attacked by the Propater and escape.

Twenty years later, the boy is the most powerful drug lord in South America. He aids his son from behind the scenes as he evades and eventually with the help of mercenaries from Nomad (some of them former Propater operatives) fights the Propater. As the plot develops focus shifts away from the main character and develops many sub-plots dedicated to terrorism, Human-improvement, the struggle of the developing countries and the power battles between the drug cartels and Propater.

Based strongly on Gnostic mythology, all major characters are named after gnostic deities, and have analogous roles.

The first 14 volumes of Eden: It's an Endless World! were published in English by Dark Horse from November 2, 2005, to April 23, 2014, before the manga was dropped. It was also released in Brazilian Portuguese by Editora JBC in 2-in-1 omnibus volumes from July 2015 to November 2016; and in Polish by Egmont from 2002 to 2009.