The episode reveals more about Krycek. His parents were cold war immigrants as revealed in the season 4 episode "Tunguska" which is how Krycek learned to speak Russian.
Apparently, in the episode, it is revealed that Krycek's father was a Russian soldier who was executed for espionage (sounds similar to CSM's past) alongside Krycek's mother. Krycek was only 10 years old when this happened. He spent the next 10 years with the commander of the Tunguska gulag who is apparently a powerful figure in the Russian army. This man was reportedly a friend of Krycek's father, but also authorized his execution. He regretted having to make that choice which is why he is repaying by caring for Krycek.
The episode opens with the executions of Krycek's parents in 1979. In 1999, Krycek assembles a meeting in St. Petersburg. Attendants include Vasilly Peskow, the gulag commander, and other people who are hard to make out. Krycek says he knows he's betrayed them in the past, but he has come to tell them that he knows they are in dangerous times and that they need him. He says he will tell them everything about his past so they will know where is loyalties lie.
In 1991, Krycek is called to a secret meeting in St. Petersburg. The gulag commander (whose name is not given) is among the people at the meeting, including Vassily Peskow (who also appears briefly in the finale). Krycek is told about his father and is asked to carry out a mission. He is sent undercover as an American soldier stationed in Saudi Arabia during the Persian Gulf War. At this point, Krycek apparently knows nothing about the black oil virus (Purity) or the Project. His job in Saudi Arabia is to learn more about America's biochemical weapons project. He is told that there is a contact that he is to speak with and that this person will contact him.
I am not sure how this part of the episode plays out. Later in the episode we see that the person Krycek was meeting with is Marita Covarubias who is working in the United Nations. She arrives in Saudi Arabia and brings him back to the US. Krycek realizes that she is collecting information for the Russians. He is taken back to the United States where somehow he learns more about The Project (although not much is given and there is no mention of aliens).
Krycek is led to an office in New York where he meets with a few members of the Syndicate. The Well Manicured Man is there with Marita. They reveal that Marita is actually a double agent who is feeding false information to the Russians and is giving the Syndicate information on them. Marita sees potential in Krycek (although she is also attracted to him) and proposes that they keep him rather than kill him. Apparently WMM agrees because the episode flashes forward 3 years later to 1994 when he is assigned as Mulder's partner. There is a scene with him in a meeting with the WMM who explains that he will go undercover as an FBI agent to keep tabs on Mulder's work.
After Scully is abducted, we see Krycek in a room overseeing tests. Flash forward several years (probably 1995 or 1996) and we see Krycek meeting with a Russian soldier (most likely the one scene in the Tunguska gulag in the episodes entitled "Terma" and "The Red and the Black".) Krycek is apparently in touch with the Russians again. Krycek says he has a digital tape that contains all of the information on the Project. By this point, Krycek is willing to return to the Russians because he now is aware of the impending invasion and wants to help the Russians resist.
The episode is not expected to mention anything about Krycek's stint with the militia (Tunguska/Terma). We are given a little more information about his relationship with Marita and we are expected to see them kiss at least once. They do have a discussion about the project (I wasn't able to determine the year this takes place). He says he believes the syndicate may have been deceived. She merely says that she knows he is in touch with the Russians and that she isn't everything he thinks she is (she is implying that she agrees with him).
We also see that Krycek still has the alien relic, known as a magic square, from the episode "Biogenesis". He knows it is valuable beyond simply proving the existence of alien life. He knows that it has power that can be given to certain people. It may be the only thing that can stop the invasion. (Krycek's plan isn't made clear).
In the final scene we see Krycek sitting in the dark meeting room in St. Petersburg. Marita is at the meeting, along with the gulag commander, Vassily Peskow, and a few other people. At this point we realize Krycek brought Marita to St. Petersburg after the episode "One Son". She has been working with the Russian/Rebel resistance. They say that they have already given the rebels what they want- the vaccine. Marita says that the rebels have revealed that the colonists are preparing to come to Earth. (This is what happens in the finale.)
The word REBELS isn't supposed to actually be spoken. The Russians only make references to them. We also shouldn't expect to learn anything new about the murder of Mulder's father or Scully's sister. Either it isn't addressed, or we are shown scenes from those episodes but nothing new is given. I don't know anything else about the plot of this episode. From what I've learned, William B. Davis (CSM) is not in the episode at all. Neither is Steven Williams (Mr. X), Jerry Hardin (Deep Throat), Peter Donat (Bill Mulder), or Mitch Pilleggi (Skinner) even though they were all major players during the time Krycek is shown working in the US.
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