In "Piper Maru," we find out that Krycek has hidden the digital tape in a locker at an ice-skating rink in the DC area. He's either found a way to un-encrypt a tape the FBI's finest couldn't decode, or he's selling Consortium secrets he knows about in other ways. This seems like a foolish thing to do, since keeping the Consortium's secrets is the only insurance he has against CM's assassins. However, it appears Krycek has fallen on hard times indeed, and needs the money.
Through information broker Jeraldine Kallenchuk, Krycek sells the French government the location of a UFO that was shot down during WWII and crashed in the Pacific Ocean. The French salvage vessel Piper Maru arrives too late, however; CM's people have already retrieved the UFO and hidden it in an abandoned missile silo in Black Crow, North Dakota. But the French do find the occupant of the UFO, an alien creature that can enter into people and possess them. It possesses Gauthier, a diver on the Piper Maru, and then his wife, Joan. From them, it apparently learns that Krycek is in Hong Kong and might know where its ship was taken. The alien then goes seeking Krycek, in Joan Gauthier's body.
Meanwhile, Mulder is seeking Jerry Kallenchuk, whom he suspects sold the information about the UFO to the French. He goes to Hong Kong and finds her eating dinner at a restaurant. He handcuffs her to himself, and drags her back to her office. Krycek is waiting there -- with a gun, even though guns are illegal in Hong Kong. Krycek shoves Jeraldine out into the hallway and locks the door. Since she's still handcuffed to Mulder, it effectively immobilizes both of them. But there are French agents out in the hallway -- pursuing Jeraldine, or the alien, or Krycek, it's not clear. They shoot Jeraldine, and Krycek escapes out of the window.
Mulder manages to unlock the cuffs in time to escape the French agents. Krycek is long gone, but Mulder guesses where he's headed. He waits at the airport, and sure enough, Krycek turns up there, apparently interested in Flight 1121 to DC. Mulder ambushes him, takes his gun, and beats him up -- for his father, for Scully, for himself. (Oddly, no one seems to notice this brawl, even though it's in a quite public section of the airport.) Krycek offers to give Mulder the tape if Mulder lets him go. Mulder agrees to travel to DC with Krycek to get the tape, then sends him into the bathroom to wash the blood off his face. In the bathroom, Joan Gauthier accosts Krycek at the urinal. It's the alien, and it wants Krycek's knowledge -- and his body.
When Krycek comes out of the bathroom, there are black, oily swirls in his eyes, meaning there's an alien on board. Mulder does not notice, however. They fly back to DC together and get a rental car. Mulder makes Krycek drive, but they do not reach their destination. CM's men run them off the road. They drag Krycek out of the car, perhaps meaning to kill him. But the alien is capable of defending itself, and fries them all with radiation. Mulder is more seriously injured than Krycek (perhaps because the alien protected or healed Krycek, perhaps because the car had a driver's side airbag only); while he's hospitalized, Krycek retrieves the tape from the locker, and goes to visit CM. The alien, in Krycek, offers CM the digital tape back in exchange for the location of its ship. CM accepts the offer.
Mulder and Scully find out from Luis Cardinal, who was with CM when the deal was struck, that Krycek will be headed for the missile silo in Black Crow, ND. They try to find him, but CM and his men chase them off.
CM locks Krycek in the silo with the UFO. The alien leaves Krycek and goes back into its ship. Krycek is left pounding on the door, screaming to be let out.