The episode begins when Scully is being held in court before Congress apparently to enlighten the commity on Mulder's current whereabouts as he is missing. When Scully refuses to give them any answers as she believes it would endanger Mulder's life, they threaten her saying that she will be put in jail if she refuses to answer the question once more.

In a flashback to two weeks earlier, we see a government official going through customs. He seems reluctant to be checked out and refuses to open the unmarked briefcase he is carrying saying that "he doesn't have the combination". After they strip search the man, he is placed in a room with the customs official who has managed to open the briefcase. Despite warnings that opening the canisters within the briefcase will endanger their lives, he still does so and clumsily smashes it open on the ground. Suddenly, a series of oily worms emerge from the broken glass burrowing into his body and into his eyes where we see a cloudy blackness form. Suddenly we are reminded of the horror shown in Piper Maru and Apocrypha.

Mulder and Scully are at a remote location, Mulder having received anonymous receipts detailing the exports of illegal bombs. The location where they are to be exchanged is here. The agents as well as a few other members, storm the scene when the truck arrives just managing to avoid being shot but the truck attempts to make a getaway. At the sound of a gunshot, the truck swerves and crashes. The driver is dead but the man who shot the driver is none other than Alex Krycek.

Krycek claims that he was the anonymous tipster and that he escaped from the missile silo with the group of revolutionaries. Mulder doesn't want to hear from him but allows him to tag along at an airport where a diplomat is arriving with evidence that could expose the crimes that they are committing. The agents manage to gain possession of the diplomatic bag he was carrying and find that the contents is just a plain old rock.

Now at Skinner's new appartment, Mulder drops Krycek off providing a safe haven for him. Skinner immediately grabs Krycek hauling him against the railings of his balcony and handcuffing him to them. Meanwhile, Mulder and Scully travel to NASA Goddard to get the seemingly useless rock analysed and they make a startling discovery, the rock could indeed be from Mars.

While this is happening, the diplomat from the airport breaks into Skinner's appartement while watched by Krycek still on the balcony. Sensing that someone is outside he comes out but to be hauled over the railings by Krycek. Skinner is interviewed under suspicion but is soon let off the hook while Mulder enters his appartement and releases Krycek taking him to where Mulder's new informant lives. After a short time, she is able to direct Mulder to Tunguska, Russia where the same rock that Mulder discovered is being dug up and people are being experimented on.

Meanwhile, the scientist at NASA Goddard is taking a core sample of the rock when it suddenly bursts open with some kind of unknown oil. The oil quickly transforms into the tiny worms seen in the customs room which sends the scientist into an immediate coma state. Scully and Agent Pendrell investigate what happened to the scientist and find he is in fact alive so they remove him from the containment room. Later, Mulder takes Krycek to the airport where he is about to leave Krycek alone in the car when he finds out that Krycek actually speaks Russian so this persuades Mulder to allow Krycek to again tag along.

While in Russia, Mulder and Krycek get captured and thrown in a cell after witnessing what looked like a torturous mining camp. Krycek, using his Russian language ability, is able to be let free from the cell but Mulder is soon injected with a substance that sends him to sleep. When he wakes up he finds himself in a large room, trapped under some metal wire stripped almost naked. As screams echo from all around him, a black fluid is poured on his face turning into hundreds of oily worms and into his nose. As we watch his eyes are clouded over with the black fluid and he is left paralysed beneath the metal gauze....... To be continued.