When Mulder leaves Doggett in the X-Files office you can see a picture of Samantha on the desk. Mulder wouldn't leave the FBI without it.
"Vienen" is Spanish for 'They Come'.
Mulder: You're sitting on the answer, Scully. The body. You find the virus, you can find what kills it.
Scully: And what if I can't?
Mulder: Well, when he gets old enough, you tell the kid I went down swingin'.
Mulder: That is the Deputy Director calling to tell you there is no need to see you. That the blame has been properly assigned for what happened out on that platform. I'm out. 86'd, Agent Doggett.
Doggett: What do you mean. You're out of the FBI?
Mulder: Kersh could barely contain his happiness. He stuck it to me.
Doggett: So, you taking the fall?
Doggett: Not for me?
Mulder: For you. For the X-Files. You're all the credibility this office has left. You have Kersh's ear and you have seen it now. Out on that platform. You saw it for yourself.
Mulder: I think he wants us to jump.
Doggett: Now, wait a minute Agent Mulder, I'm in charge here. On two count.
Mulder: How about a 20 count?
Doggett: One! Two!
Kersh: I obviously haven't been able to rely on those whose job it is to keep me apprised and informed. I have to rely on phone calls, like the call I received from Martin Ortega. Why doesn't somebody make me privy to who the hell gave the order to shut down that rig.
Skinner: I did.
Kersh: Well I'm giving the order that this quarantine is lifted.
Scully: We could do that Sir, but all radio contact has been cut off.
Kersh: As soon as it's re-established I want that rig up and running, and the entire crew choppered off the Galpex-Orpheus and debriefed.
Scully: Sir, I think that would be a mistake ...
Kersh: I think it would be a mistake not to, Agent Scully. And you're running out of mistakes, both you, and the Assistant Director. If I didn't know better, I'd say this was a Mulder stunt.
Doggett: Agent Mulder, don't walk away when I'm talking to you. Like it or not I've been assigned this case. One call to the Deputy Director and your up for insubordination.
Mulder: How are you going to call when the radio's broken?
Doggett: Don't push me Agent Mulder.
Mulder: You won't do it.
Doggett: You think?
Mulder: We're both in the same boat, Agent Doggett. We're just paddling in different directions.
Doggett: No we're not going in different directions here, we're going in one direction. My direction.
Doggett: I never would have believed it. These stories about you.
Mulder: Really, what stories are those?
Doggett: That you can find a conspiracy at a church picnic.
Mulder: How'd you get stuck down here, Agent Doggett? Kersh catch you peeing in his cornflakes?
Mulder: Answer the phone, Agent Doggett. You're in charge here now.
This episode is the last one where Mulder was officially an FBI agent and the last scene of this episode shows the last time Mulder is seen in his basement FBI office.
This is the only mention and appearance of the Black Oil in Season 8, it is also the last. It would be later referenced in flashbacks during the series finale in Season 9. The apparent changes in plot are obvious as the writers seem to be doing away with former plot lines and adding new ones (ex. the Super Soldiers).
As Mulder and Doggett prepare to leap from the burning rig, they hesitate and agree to go "on two". According to producer Paul Rabwin on the DVD commentary, this was a homage to Butch Cassidy and the Sundance Kid.