An archaeological team finds a sealed cave on a mountain side in Costa Rica, containing ancient remains. But upon entry, the body disintegrates and infects the team with an ancient virus.
Dr Edward Marcase, a paranoid but brilliant virologist with mystic views, is called in. The White House has created a top secret team to deal with unusual and/or unexplained outbreaks of viruses on American soil. Marcase discovers the other doctor on the team, Dr Kimberly Shiroma, holds him directly responsible for the death of her fiance. Responsible for security is Agent Michael Hailey.
One of the infected archaeologists, Glynden, has been captured but the other is still at large. The possessed archaeologist tells of an ancient super-virus which once covered the globe until a world-wide flood destroyed almost all their kind. A virus which controlled the other major viruses - which possessed Humans but co-existed with them, using other viruses to kill the weak but strengthen the survivors. The virus acts like a hive-mind, allowing it to communicate with other infected persons.
Marcase and Shiroma discover bacteria in the ancient ocean destroyed the super-virus and they then use it to destroy the infection. They believe the virus destroyed. But later, we see the area where the virus was found and see butterflies suggestively moving as a group... and a monkey with bloody eyes.