Rainbow is a newly formed anti-terrorism organization headquartered in Hereford, England, the same location as the British Secret Service base. This multi-national team consists of highly-skilled military and intelligence officers who are able to quickly mobilize when called upon for assistance. Rainbow is a "black operation" that stays in the shadows and only responds to a terrorist situation at the request of a country's government. The organization is led by former CIA agent John Clark, code name Rainbow Six.

John Brightling, the wealthy CEO of an American pharmaceutical company, Horizon Corporation, has secretly hired a former Soviet KGB agent, Dmitriy Popov, as a consultant. Popov's role is to instigate a new wave of terror incidents across Europe. Popov will accomplish this by offering large payouts to contacts from the old terror network with whom he dealt in the past. Brightling does not provide Popov with the underlying reason for this operation.

Popov does his job and stirs some old terrorists into action in several incidents across Europe, all dangerous situations involving hostages. Rainbow is called in and is able to take down the terrorists without harm to the hostages. Upon reviewing tapes of the incidents, Popov spots specific similarities convincing him that the "police" responding in the incidents are in fact actually a sophisticated para-military operation and not local law enforcement. At the same time, Rainbow suspects that there is a super terrorist behind the scenes stirring up the old terrorist network. Each side endeavors to discover the other, unwittingly working toward one another.

John Brightling and his dedicated group of followers are environmental radicals. They feel the earth is being ruined by humans and want to see it returned to nature and animals. Horizon Corporation has developed an Ebola-like flesh eating virus called the Shiva virus. The effectiveness of the virus is tested on humans nabbed off the streets of New York City. The diabolical plan is to spread the Shiva virus world-wide, eliminating most of mankind. Horizon has developed an anti-Shiva vaccine which will be administered to only a select few chosen by Brightling.

The target location for launching the deadly virus is at the Olympic Games being held in Sydney, Australia. A follower of Brightling, Bill Henriksen, is a security consultant who is attempting to win the security contract for the Olympic games. Henriksen plans to use the recent high-profile terrorists incidents as leverage in attaining this contract. Once attaining the security detail, Henriksen's people will plant the breathable Shiva virus into the cooling system. The infected athletes and spectators will travel back to their home countries and spread the highly contagious organism on a world-wide basis. There will be a new world order. Nature will be the dominant force on earth and man will be whittled down to just a select few True Believers.

Clark and Popov both make progress in discovering each other. Brightling and Henriksen become concerned that Popov's identity will be exposed and potentially destroy their plans for the Shiva pandemic. Popov is whisked off to Horizon's new complex in Kansas where human survivors will gather after the epidemic is in full force. At the complex, Popov is finally able to learn the reason Brightling dispatched him to instigate terrorism and the full details of the Shiva Project. He is so appalled that he escapes and contacts John Clark. In the eleventh hour, Rainbow is able to thwart the vile plans of John Brightling.