Green Legend is set in a science fiction-style post-apocalyptic Earth, which has turned largely into a vast desert after an alien invasion, in which six of the "Rodo" (a race of what appear to be giant monoliths) crashed onto Earth from space, somehow effecting massive climate change which has completely wiped out the oceans and rain. At the time, mankind was ruining the environment, making an apocalypse of some sort inevitable (similar to other environmentally-focused anime like Nausicaä of the Valley of the Wind; in general style, Green Legend is much like Nadia: The Secret of Blue Water and Future Boy Conan). In this brutal new world, two polarized factions have arisen: the first faction, the "Rodoists" are a fanatical religious sect who worship the Rodo while practicing hydraulic despotism; all communities are clustered around one of the monoliths, as they are the only remaining sources of water and food - most of which is gathered quite close to the monoliths in what they call the "Holy Green". Travel between communities is infrequent, as at a certain distance from the monoliths, the environment peters out to the point that the air itself cannot be breathed - necessitating pressurized vehicles akin to spaceships. The second faction, the "Hazard", is a secretive revolutionary movement opposed to the Rodoists. The protagonist (Ran the greener) is a young orphaned boy who seeks to survive, to join the Hazard, and to find and take revenge upon the man with a scar on his chest who killed his mother. He blunders into the middle of a battle between the Hazard and the Rodoists, during which he meets a strange silver-haired girl named Aira. Ran helps some Hazard scouts escape his town and joins them. Soon, the Rodoist army attacks the Hazard base; Aira is forcibly evacuated against her will by the Hazard. Ran attempts to board the sand ship, but fails, and begins pursuing it across the desert in a stolen pressure suit. He is rescued by traveling water and food merchants just before his air runs out. The merchant leader, a contemplative man named Jeke, offers Ran his assistance in rescuing Aira. The rescue goes awry when the Rodoists attack the Hazard sand ship and recapture Aira as Ran and the merchants attempt to infiltrate the same sand ship.