When a plague is unleashed in a prison and starts killing a lot of people, Mulder and Scully must try to stop it only to find out why exactly they were called out in the first place.

Dr. Robert Torrence, a scientist finds the carcass of a wild boar out in a rain forest in Costa Rica and suddenly gets sprayed by an unknown liquid while taking samples. Hours later, he radios for help but dies when a sore which has developed on his face explodes. In the morning, he is discovered as vultures eat away at his remains.

Later, a convict of the same name receives a package containing the bloody leg of a wild boar. Just 18 hours later, he is rushed by a group of white-suited specialists to an operating theatre, covered in boils just waiting to burst..............ewwww!!!

Meanwhile, two more convicts escape from the prison when they realize that their lives may be in danger. Mulder and Scully though, are probably the only ones entering the prison to find out just what is going on but are suspicious when they discover that it isn't really the escaped prisoners that are the real problem.

The agents decide to part, Mulder searches for the convicts while Scully attempts to find out what exactly is going on in the prison. She finds out little though from an unhelpful scientist named Dr. Osborne who only tells her that he is from the CDC (Center for Disease Control) and that out of 14 men infected, 10 of them have died already. This shocks Scully who soon discovers more bodies being incinerated. When Osborne discovers Scully nosing around, he is suddenly squirted by the liquid from a burst pustule and so runs off in terror. Soon later, Scully learns that the package was sent by Pinck Pharmaceuticals, a drugs manufacturer and discovers a dead insect in one of the pustules.

Meanwhile, Mulder searches for the convicts along with the men from the US Marshal's office and finds Paul's girlfriend (one of the convicts), Elizabeth in a house but with Paul long gone and Steve (the other one) dead in the bedroom having been infected and killed by the short term virus.

Later, Dr. Osborne confesses that he actually works for Pinck and that he is infected himself. He also adds that the company had financed the exploration of new drugs and were testing out the effects of the virus in the confined area of the prison and that they found the parasite, F. Emasculata which contains the deadly virus. Also he says that she must try to warn people of what is happening but when he dies, she is left to fend for herself although it seems that the truth will never ever come out.

Mulder, on his own, goes to visit Skinner and tells him that they must warn the public of the killer disease but encounters the Cancer Man who says they must "control the disease by controlling the information". Mulder doesn't want any part of the cover-up but according to the Cancer Man, he is already a part of it.

Mulder goes to speak to Elizabeth but she is reluctant to answer any of his questions. He does finally get the location of where Paul is heading to (he is infected himself) and that he has boarded a bus for Toronto. A dozen armed men surround the bus, as Mulder boards trying to get the truth out of him but as a pustule on his face is about to erupt a shot is fired, he is killed and is whisked away by 'the men in white suits'.

As the agents talk with Skinner about wanting to go public with the information he replies that they "never had a chance" and that because the scientist and the convict had the same name, the whole thing was going to be blamed on a simple 'mistake'.

"Watch your back," Skinner tells them as the agents leave, "This is just the beginning".