He refers Mulder back to the Voyager probe which was sent into space to look for intelligent life. Apparently, though the project has been shutdown, they have reason to believe that contact was made and that a UFO retrieval team has been dispatched to collect any evidence and perform a clean-up operation within 24hours. Mulder heads off on his own to try to collect any evidence he can before the team can destroy it all. He receives a phone call from an unknown source who tells him "You have a friend in the FBI." The source implies that success on this case is imperative to the re-opening of the X-Files. This source will turn out to be the character known as Mr. X...or just X. we see a clandestine meeting between Krycek and CSM in which Krycek reports Mulder's meetings with a new source (X) and that Scully is a bigger problem than they thought. Scully seems to be helping Mulder despite the fact that they are no longer problems and CSM's response to Krycek is, "Every problem has a solution."

Little Green Men Season 2 opens with the partners reassigned; Mulder is working wiretap surveillance and Scully is teaching at Quantico. When Scully is in the FBI building she sees Mulder in the hallway and he doesn't acknowledge her or even seem to see her. She leaves him a sign that she wants to meet with him and they do so that night in the Watergate parking garage. Mulder tells her they should assume that they are being watched and shouldn't meet unless it is something important. Scully is just worried about Mulder since he seems to have lost his drive to search for the Truth. After Scully leaves him in the garage, he flashes back to his sister's abduction. We meet one of Mulder's "contacts in Congress" who he had referred to in the pilot in the form of Senator Matheson, an insider who seems to be interested in helping Mulder. He refers Mulder back to the Voyager probe which was sent into space to look for intelligent life. Apparently, though the project has been shutdown, they have reason to believe that contact was made and that a UFO retrieval team has been dispatched to collect any evidence and perform a clean-up operation within 24 hours. Mulder heads off on his own to try to collect any evidence he can before the team can destroy it all. While there, a bright light floods the room and Mulder sees a figure which might well be an alien. The following day, Scully, who has caught up with Mulder, finds Mulder unconscious minutes before the retrieval team arrives (incidentally they have orders to shoot to kill if necessary). There, in the form of tapes and printouts, is evidence that will prove the existence of extraterrestrials. But with no time to lose and the team just driving up the road, Mulder and Scully have to leave and Mulder only has enough time to grab one reel of audio tape. They escape safely in a close call, but when Mulder plays the tape back he finds it blank meaning that he still has no evidence. Mulder gets chewed out by Skinner for abandoning his wiretap but when Mulder responds by saying his phone was illegally tapped, Skinner's anger is turned on CSM who was silently standing by during the dressing down. At the end of the episode, Mulder tells Scully that despite the lack of evidence, he still has the X-Files and he still has Scully. The Host The case in this episode is not important to the mytharc but it is the first time we learn that Mulder has a new contact. He receives a phone call from an unknown source who tells him "You have a friend in the FBI." The source implies that success on this case is imperative to the re-opening of the X-Files. This source will turn out to be the character known as Mr. X...or just X. Another interesting aspect to this episode, is that the case is given to Mulder by Skinner. He is pulled off his wiretap and sent to investigate a case that would have normally fallen under the category of an X-File. This is the second instance (including the support he received in Little Green Men) of Skinner trying to help Mulder by providing him with a case and in effect supporting his interest in the X-Files and the Truth they contain. Sleepless In this episode, Mulder is assigned a new partner and a new case involving secret sleep deprivation experiments carried out on soldiers during the Viet Nam war to create a better soldier. The case itself points to more government tampering in unsanctioned experiments but the real importance of this episode to the mytharc is the assignment of Alex Krycek as Mulder's partner. He seems too darn squeaky clean to begin with and Mulder doesn't trust him farther than he can throw him and makes it perfectly clear to Krycek that he doesn't want him as a partner. But by the end, Krycek's constant brown-nosing and glorification of Mulder as a great FBI role model starts to wear Mulder down and he seems to accept Krycek at face value. This case includes another contact with X, in which he tells Mulder, "The truth is still out there, but it's never been more dangerous." Mulder doesn't realize how true this is because at the close of the episode, we see a clandestine meeting between Krycek and CSM in which Krycek reports Mulder's meetings with a new source (X) and that Scully is a bigger problem than they thought. Scully seems to be helping Mulder despite the fact that they are no longer partners and CSM's response to Krycek is, "Every problem has a solution."