Scully comes to believe that post-abduction Mulder is not dead but in a kind of chrysalis state that, if left untreated, will turn him into a murderous alien. The finale, in which the two agents are finally reunited, is a tear-duct-stoking tour de force.
Mulder and Scully's nemesis Alex Krycek (Nicholas Lea) returns with tales of a rock containing the black oil alien introduced in "Piper Maru"/"Apocrypha." This episode and the follow-up, "Terma," feel especially epic in scope -- Mulder winds up at a Russian gulag producing a black oil antidote -- even if the mythology is starting to get somewhat narratively senseless.
In the conclusion to "Tunguska," a long-retired KGB agent is tasked with destroying the rock containing the black oil virus. Mulder, meanwhile, escapes from the Russian gulag, returns to help Scully deal with a Congressional inquiry panel, and then does everything possible to get that rock back. Deliriously entertaining, no more so than when "ratboy" Alex Krycek, in a beautiful bit of poetic justice, loses an arm.