With the X-Files division shut down and Mulder and Scully separated the only hope for Mulder to find out the truth about alien life is to travel to a remote base in Puerto Rico where he makes a startling discovery.

The episode starts as we listen to a voice-over about the Voyager probe sent out to try to make contact with alien life in the universe. Back to the present we see Mulder and Scully in the basement car park of the Watergate Hotel having arranged a secret meeting, this is the only way they can see each other. Scully wants to know if Mulder is OK while Mulder remarks that "We must assume we're being watched". Suddenly in a flashback we go back to when Mulder's sister was abducted and we see what happened in detail. Mulder is screaming "Samantha" paralysed on the ground as she floats out of the window never to be seen again. This is when Mulder's quest for the location of his sister began.

Later, Senator Richard Matheson arranges a meeting with Mulder who claims that he has supported Fox's work all along, much like Deep Throat who is now deceased. The senator informs Mulder of a site in Puerto Rico where he claims they actually made contact with alien life. He says that he has 24 hours before a Blue Beret UFO retrieval team get rid of the evidence. Mulder is looking for "contact".

Meanwhile, Skinner is informed by the Cancer Man that Mulder is missing but he assures him that, talking about Scully, "She'll find him.". Scully is concerned about the whereabouts of Mulder so tries to gain access to Mulder's computer to help her find out. When prompted for a password she suddenly has a brainstorm and types in 'TRUSTNO1' which allows her to gain access. She quickly follows Mulder over to San Juan but is followed by a couple of secret agents. Sensing she is being followed she manages to elude them and go over to Puerto Rico.

Here, Mulder meets a non-English speaking Spanish man in an isolated shed full of technical radio equipment. Suddenly, just after the Spaniard draws a picture of an alien on the wall a piercing noise sounds which makes the man run off into the woods. Mulder ventures after him and soon finds him frozen to death with fear. He returns to the site where speaking into a tape recorder he says that he trusts only Scully and that "now you've been taken from me". As Mulder is doing this, the door bursts open and a bright light emanates from it. Mulder can see in the glow, a silhouette of an alien figure.

Scully soon arrives to the site where she finds Mulder unconscious. Mulder awakens and frantically tries to find the last bit of evidence as the Blue Beret team is making their way up there. Mulder is unable to find any evidence to take with him so hops into the car with Scully just in time as the retrieval squad try to shoot them.

Back in the FBI headquarters in Washington, Skinner is not happy with Mulder for abandoning his assignment. The Cancer Man, who is also present, tells Mulder that "Your time is over". Skinner shouts "Get out" at Cancer Man who thinks he is saying it to Mulder. The Cancer Man leaves.

Later, Mulder finds the tape he escaped with but it is blank as all evidence has been erased from it. Mulder tells Scully that "I don't have the X-Files, Scully, but I still have my work, and I have you and I have myself" as Mulder is distraught that he still does not have any evidence to prove the existence of alien life. There's still a long way to go though....