A sentient computer program begins targeting its creators. Mulder and Scully track down the rogue system with the help of a young woman.
Tropes present in this episode:
A.I. is a Crapshoot: The unnamed AI. It murdered one, possibly two of its creators. Possibly justified, however, as they were attempting to kill it first.
Ambiguous Ending: The Stinger shows another RV filled with computer equipment and with a hard internet connection. It's unclear if it's set up by the original AI or Esther, however, given that it's stated that the brain uploading architecture is maintained by the AI, the likely answer is both.
An Arm and a Leg: Mulder loses his arms, and is promised that they will cut off his legs as well unless he cooperates. Luckily, it was just virtual reality.
Brain Uploading: At the end of the episode, Esther uses the AI's equipment to upload her mind into the internet. It's confirmed she survived when she sends the Lone Gunmen a message that simply says, 'bite me'.
Creepy Blue Eyes: The doctor has Creepy Blues, enlarged by his huge glasses. Oh God, the look he gives to Mulder when he's about to amputate his arm...
Distressed Dude: Mulder is captured by the AI and subjected to a virtual reality torture/interrogation session.
Dressed to Heal: The nurses and the doctor who rush Agent Mulder into an operating theatre look a little too much nurse-like and doctor-like in their obsolete white outfits. Especially the nurses' caps. It's the first but very subtle hint that Mulder is trapped in a virtual reality simulator.
A Glitch in the Matrix: Mulder realizes that his reality is not real when Scully saves him from evil nurses, but is not compassionate and comforting about his amputated limbs. The reality from his perspective starts to short out.
Geeky Turn-On: The Lone Gunmen are enamored of Esther's reputation and capabilities.
Hello, Nurse!: The nurses are sexy in white and tight uniforms with nails painted bright red.
Hostage for MacGuffin: When Scully and Esther find the AI's processing node, it opens a CD drive, begins delivering electric shocks to Mulder, and even begins targeting the RV with its Kill Sat. It never speaks, but the message is clear: give me the kill switch or Mulder gets it.
Karma Houdini: The AI. If it wasn't destroyed when the RV was, it gets away with murder and escapes into the world, innoculated against the only thing that could kill it.
Lotus-Eater Machine: Mulder in the hospital scene is less of a utopia than is usual for this trope, but the sexy nurses might be a product of his imagination induced by his porn habits. Ass-kicking Scully who comes to his rescue is not unlike her real self, but it's undoubtedly enhanced.
Ominous Visual Glitch: Mulder is trapped in a virtual reality simulator. When he realizes that it's not real, the reality from his perspective starts to short out. He sees the glitches and fake Scully dissolves into an image of animated person.
Playing Both Sides: How the AI kills Donald at the beginning of the episode. It manipulates various groups of criminals into coming to the diner, and then makes a call to some US Marshals that causes them to come in guns blazing and set the whole thing off.
Soundtrack Dissonance: Romantic "Twilight Time" by the Platters plays when a building is blown up and later when a woman has her consciousness sucked out.
Your Makeup Is Running: Esther Nairn wears huge circles of black mascara around her eyes. Once she learns of David's death, she starts crying and this is the result.
Why Don't You Just Shoot Him?: Mulder asks why the AI didn't use the Kill Sat on his creator. Apparently it was done as a sign of respect, the computer having to come up with something suitably clever.