In a post-20th century world, nuclear and biological warfare have wreaked havoc on the natural environment, causing widespread contamination and extinction. The planet is on the brink of the "Big Six," the sixth mass extinction event. In response, humans have constructed sky cities to shelter endangered species and allow for genetic crossbreeding and evolution. The inhabitants of these cities have formed their own civilization, detached from the world below. However, when Kui, Hiruma, and Root stumble upon a lone plant seed, their curiosity leads them on a perilous journey to the ground below, unaware of the irreversible consequences.