- Actor Allusion Piper Maru is actually the name of Gillian's daughter.
- Black Eyes of Evil: Those who were black oiled.
- Body Horror
- Buried Alive: Discussed.Johansen: We bury our dead alive, don't we?
Scully: I don't know if I understand.
Johansen: We hear them every day. They talk to us. They haunt us. They beg us for meaning. Conscience... it's just the voices of the dead trying to save us from our own damnation.
- The Conspiracy
- Flashback: Commander Johansen's account of what happened in the submarine.
- Government Conspiracy: The French Government was involved this time.
- Happy Flashback: Scully sees herself and Melissa playing hopscotch.
- It's Personal: Scully gets very angry when she finds out that they are trying to stall her sister's murder investigation.
- Monochrome Past: Scenes in the sub were shot in black and white.
- My God, What Have I Done?: Johansen knew the moment he sealed the door that he was sealing the fates of the men on the other side.
- Myth Arc: The first episode to feature the black oil.
- The Reveal: The final shot of the flashback shows that Captain Sanford had been taken over by the black oil.
- Sadistic Choice: With the submarine crew getting sick and frustrated, Johansen was faced with either continuing to obey Captain Sanford's orders or leading a mutiny. When the gunshot disrupted their silent running, Johansen made the choice to take command.
- Spanner in the Works: The panicky crewman firing a gun during silent running. Doing so led Johansen to act and disrupted the black oil's quest to find the ship.
- The Virus: The black oil.
- Wham Shot: Captain Sanford having Black Eyes of Evil.
- Krycek emerging from the shadows in Hong Kong.