The book is set in the not-so-distant future, where humankind has all but succeeded in controlling all life on the planet and almost completely wiping out all insect life. The earth is divided into a "Green Zone" which humans totally dominate (or so they believe) and a diminishing "Red Zone" that is not yet conquered.

The "Green Brain" of the title is an intelligent organism that embodies and arises from nature's resistance to human domination. It is able to command social insects to form humanoid-shaped collective organisms which it uses to infiltrate the "Green Zone".

The book is about a small team sent into the jungles of Brazil to investigate the problem, who find out that some of their assumptions were wrong.