This is the 3rd and final part to a trilogy of episodes that started with the previous season finale. This one is a little different that the other two in that much of the episode is a dream that Mulder is having while being treated for his condition.
The Smoking Man and Mulder’s mother check Mulder out of the hospital and have him transferred to a government facility. Meanwhile, Scully learns that Mulder’s condition is possibly caused by the alien artifact reawakening the alien virus Mulder was exposed to years previously. This helps parts of the previous two episodes seem a little less contrived but for enjoyment of the episodes it might have helped to have learned that little tidbit earlier. At the government facility, they operate on Mulder to remove the infected tissue and transplant it to The Smoking Man who believes it will enable him to survive the coming alien apocalypse.
It is during this that Mulder has his dream. In this dream, The Smoking Man claims to be his father and takes him to a nice suburban neighborhood where he meets some he though were dead including his sister and Deep Throat. He is led to believe he should let the world think he is dead and start a new life which he does. He marries Fowley and lives his life until he is an old man and everyone else is dead except The Smoking Man.
In the real world, Scully has a security card slipped under her door that grants her entrance to the facility where Mulder is held and she is able to rescue him. Fowley is later found dead.
I would give this episode 4/5 stars. This trilogy of episodes, while not as good as the best episodes in the mythology, serve as a good introduction to the next chapter.The dream sequence in this particular episode adds some uniqueness and foreshadows a possible world to come with the alien invasion.