In "Terma," it is unexpectedly revealed that Krycek is a Russian agent. It's not clear if he's been a Russian spy all along, or if he was recruited only after CM locked him in the silo. In fact, it's very difficult to make any sense at all out of the events of "Tunguska" and "Terma," but here goes....
It seems both the U.S. and Russia are experimenting with something they call the "black cancer." It's an alien lifeform that came to earth on a comet or meteorite that hit Tunguska, Siberia in 1908. It can be used for biological warfare, and both sides are trying to develop a vaccine against it. But since the source of the black cancer is in Russia, the Russians have a certain advantage. Krycek, who is apparently a Russian agent with a surprising amount of power, wants to keep it that way.
Using the name "Arntzen," Krycek activates a retired KGB assassin named Vassily Peskow. Peskow goes to the U.S. to remove all sources of the "black cancer." He kills Dr. Charne-Sayre, the doctor in charge of the black cancer innoculation program, and all of the patients she was testing the vaccine on. He also kills the Goddard Space Center scientist who was infected by oilien worms while investigating a Tunguskan rock, and neutralizes the truckbomb Krycek built for the militia.
Again using the name "Arntzen," Krycek joins an anti-government militia, offering to help them build bombs like the one that leveled the federal building in Oklahoma City. It appears that his only reason for doing this was to acquire some bait for Mulder. (If he really is a Russian agent, it's unlikely that he shares the ideology of this right-wing militia. Nor did he share their agenda; obviously he did not intend the bombs to actually hurt anyone, since he lead Mulder to one of them, and apparently ordered Peskow to neutralize the other.) Krycek begins anonymously sending Mulder receipts - for fuel oil, fertilizer, a rental truck, etc. - that hint that a truck bombing is about to occur. Using this information, the FBI stakes out a warehouse in Queens, arresting all the militia members as the rental truck drives up. The truck speeds away, but Krycek, who is in the passenger seat, shoots the driver. When Mulder sees it's Krycek, he hits him with the butt of his rifle, and might even have shot him if Scully hadn't intervened. Krycek then reveals that it was he who sent Mulder the receipts.
Krycek tells Mulder that the militia rescued him from the silo while on a salvage mission. And he offers Mulder information about more bombs, if Mulder will help him expose CM. Mulder can't refuse that, so at Krycek's behest, he, Krycek, and Scully go to the airport to intercept a certain diplomatic courier. They lose the courier but get his pouch, which contains only a rock. Mulder and Scully are angry, and Krycek appears surprised, but as it turns out, he probably knew all along what was in that pouch.
Mulder brings Krycek to Skinner's 17th floor apartment, and Skinner, apparently holding a grudge from the stairwell incident in "Paper Clip," punches Krycek in the stomach, then handcuffs him to the balcony railing. He's left there all night, and Skinner means for him to stay there all day, too, because he's still out there when Skinner goes to work the next morning. (!) But just before lunch time, the courier whose rock Mulder and Scully stole shows up at Skinner's apartment. Krycek slips over the railing of the balcony to hide, dangling by his fingertips, seventeen stories up. The courier comes out on the balcony, though, and Krycek is forced to defend himself by grabbing the man and dragging him over the railing balcony to his death. This causes all kinds of problems for Skinner, who has to explain to police and eventually to a Senate subcommittee what exactly was going on out on his balcony that resulted in the death of the courier.
While Skinner is talking to the police outside his apartment building, Mulder slips in to smuggle Krycek out. Krycek tells Mulder to "follow the pouch," and Mulder does, driving to New York City with Krycek to see his informant, Marita Covarubias. (This should be about a five-hour drive, but it seems to take them over twelve hours, since it's around noon when they leave Skinner's apartment, and they don't arrive at Marita's until after midnight.) Mulder leaves Krycek handcuffed to the steering wheel of the car and goes up to Marita's apartment. She tells him where the rock came from - Tunguska, Siberia - and makes arrangements for him to fly there using diplomatic papers.
It appears that Mulder is going to leave Krycek handcuffed in the car in the airport parking lot, until Krycek swears at him in Russian. Or maybe Mulder was only teasing Krycek, and planned to take him with him all along. At any rate, Mulder heads off for Russia, dragging Krycek along as an interpreter.
In the forests of Tunguska, Mulder finally tells Krycek why they're there: he thinks the rock they intercepted contains alien life, and was part of the meteorite or comet that hit Tunguska in 1908. (As it turns out, Krycek must have known this all along, but he pretends to be suitably astonished.)
Mulder and Krycek find a labor camp where prisoners are being forced to mine for fragments of the alien rock. Unfortunately, the camp's guards spot them, and they are chased down and captured. Mulder is put into a prison cell, while Krycek is taken to be questioned. When he's brought back and thrown into the cell with Mulder, he seems panicked, clawing at the door and window and telling Mulder they are going to be tortured as suspected spies. Mulder, who has been slapping Krycek around for the entire episode, slams him up against the wall and demands to know what Krycek told the guards. Krycek says he told them they were just "stupid Americans, lost in the woods." Then he tells Mulder "You're going to need me in here. Don't touch me again."
After Mulder and Krycek are served cockroach soup for dinner and decline to eat it, the guards come in to beat on Krycek some more. (Curiously, they don't lay a finger on Mulder. Perhaps it's no fun hitting someone who doesn't speak Russian? Or they feared he was someone important, since he was a foreigner?) Krycek has had enough, however, and demands to speak with their supervisor. They take him out of the cell. Once he is gone, the man in the cell next door tells Mulder Krycek has betrayed him.
Then the guards return, with a Dr. Mengele-type. They hold Mulder down, inject something in his neck, and take him away to be experimented on. Something is either injected into his left arm or removed from it; we see a blood-spotted bandage there. Oilien worms are dumped on Mulder's face, and infect him. The experience is painful but seems to cause no serious harm...yet, anyway. Mulder's neighbor tells him that it will happen again and again until he dies, and Mulder vows to kill Krycek first. The neighbor then gives Mulder a homemade knife with which to accomplish this task.
The next morning the prisoners are herded out of their cells to work, and Mulder sees Krycek standing on a loading dock, next to a truck. Krycek is talking with the doctor who experimented on Mulder; they seem to be on very friendly terms. Furious, Mulder pulls out the homemade knife and runs up to the loading dock. He knocks Krycek down into the back of the truck and punches him a couple of times, knocking him out, but does not kill him or even try to use the knife on him. He jumps behind the wheel of the truck and drives off.
Mulder makes good his escape, but finds that the truck's brakes don't work. (This particular truck, a German model designed for farm work, has something like 20 different gears, including some that are so slow the truck barely moves. But Mulder either panics and doesn't think clearly, or he doesn't really know how to drive with a manual transmission, because he doesn't try to downshift. :-) Krycek wakes up in the back of the truck, and throws himself off of it. (Either he realizes the brakes have failed, or he figures jumping off a speeding truck is safer than staying with Mulder.)
(It seems unlikely that Mulder, armed only with a knife hammered out of a tin can, could escape from a gulag that supposedly no one ever escapes. The guards had guns but did not fire them. So...perhaps Krycek had arranged for the truck to be there, and for the guards to let Mulder escape. And perhaps the guards would not have chased Mulder at all if he hadn't taken Krycek with him. It seems unlikely that the truck's brake failure was also planned, though; if they wanted Mulder dead, there were surely more reliable ways that could be made to look just as accidental.)
Nevertheless, Krycek was apparently not as happy at the gulag as he seemed to be, because he doesn't try to go back along the road. Instead, he runs away into forest. It's a costly error. He meets up with the local peasants, all of whom are missing their left arms. He asks them to help him...and they do, by cutting off his left arm.
The local peasants apparently believe that without their left arms, they are safe from being experimented on in the gulag. The reason for this is unclear; perhaps the doctors need the smallpox scar, usually found on the left arm, for inventory purposes. Or perhaps the gulag experiments are so strictly controlled that the black cancer vaccine must be given in the left arm, for the sake of consistency.
At the end of "Terma," Vassily Peskow comes home to his little apartment in St. Petersburg. He finds Comrade Krycek waiting there, dunking a teaball in a teacup using a prosthetic arm. Peskow protests that he is retired, he doesn't want to do yet another job - making it clear that it was indeed Krycek who activated him. Krycek assures him that all he wants to do is thank him for a job well done.
Alex Krycek, last defender of the left wing...even though he doesn't have one.