Central Intelligence Agency operative John Clark and Domingo Chavez join Special Air Service (SAS) officer Alistair Stanley in forming an elite multinational counter-terrorist unit known as Rainbow, based in Hereford, United Kingdom. The unit consists of a highly effective and cohesive pair of operational squads, supplemented by intelligence and technological experts from the SAS. Clark is the commanding officer, while Chavez leads one of the two squads.
The first deployment of Rainbow involves Chavez' squad in the rescue of hostages during a botched bank robbery in Bern, Switzerland. Several weeks later, Chavez is deployed to Germany, where a group of left-wing German terrorists have taken over the schloss of a wealthy Austrian businessman, Erwin Ostermann, in order to obtain imaginary "special access codes" to the international trading markets. Through careful planning and negotiating, the terrorists are persuaded to take their hostages out to a waiting helicopter, presumably to make their getaway. On their way to the helicopter, Rainbow's disguised shooters ambush and kill them.
Clark and his colleagues become suspicious about this flurry of activity from older terrorists. Unbeknownst to them, radical eco-terrorists from a biotechnology firm called the Horizon Corporation have orchestrated the previous attacks, having hired ex-KGB officer Dimitriy Popov to foment the incidents. The increase in terror attacks helps their security firm land a contract during the Olympic Games in Sydney, Australia. From within the Olympic security apparatus, they plan to launch a sophisticated bioweapon attack intended to wipe out the majority of the human race.
The conspirators, staunch environmentalists, believe that the great proliferation of humanity is destroying the biosphere and that the optimum number of humans in the world should not exceed half a million. Therefore, the "excess" billions must be killed off. The plan is to use the Olympics where people from virtually every country in the world are gathered, and infect athletes and spectators with a mutated form of Ebola which they would carry back to their countries. When the disease starts breaking out in various countries, the Horizon Corporation would announce that it had fortunately developed a vaccine and is set to produce it on a large scale, and be hailed as a savior. The world's governments would hurriedly organize giving the supposed vaccine to their entire populations. By the time it is realized that in fact it was the disease itself, it would be too late - the whole of humanity would be dead or dying, except for the "chosen few" who would get the real vaccine and who would inherit the emptied world. The fanatic conspirators, bearing no personal animosity to the billions they plan to kill, are utterly convinced of the justness of their act and think of it as "saving the world" - i.e., saving the environment and the biosphere from the encroachment of destructive humanity.
All this remains hidden in the background, while Popov learns about Rainbow - whereupon he directs members of the Provisional Irish Republican Army to take over a local hospital in Hereford near Rainbow's base, take Clark and Chavez's wives hostage, and ambush one of Rainbow's squads. Rainbow and the SAS retake the hospital, capturing some of the terrorists. Interrogation reveals Popov's involvement in instigating the attack. Now the focus of a manhunt, Popov is kept hidden at Horizon's secret base in Kansas. Upon learning about the planned Olympic attack (and realizing that he has been deceived about the true nature of his employment), an appalled Popov escapes the compound and contacts Clark. Fortunately, Chavez is present at the Olympics as a security consultant and manages to thwart the attack.
Their plans destroyed, the eco-terrorists retreat to their refuge deep in the Brazilian rain forest, hoping to negotiate a deal to return to the United States. Clark, knowing that they may never be put on trial, tracks down the Brazilian hideout and deploys Rainbow to the location. After Rainbow defeats the eco-terrorists' militia force and destroys their facility and supplies, Clark has the survivors stripped naked and left to die, taunting them to "reconnect with nature." When no survivors resurface in nearby towns, one agent notes that although people try to preserve nature, nature is not known for returning the favor.