When people in Mainframe, including Dot, start going missing, Bob sets out to find them. Along the way, the enigmatic Mouse has her own agenda ...

This episode has examples of:

• Acid-Trip Dimension: When the portal to the Web appears, it is filled with constantly shifting fractal-esque spiral patterns, mirroring the form of the Web creature on a much larger scale.
• Adam Westing: Gillian Anderson guest stars as Data Nully, a parody of her X-Files character Agent Dana Scully.
• Affectionate Parody: The entire episode plays off The X-Files, including expies of Mulder and Scully with binomes Agent Modem and Agent Nully.
• Apocalypse How: Of indefinite class; the bomb placed by the Guardians is powerful enough to destroy all of Mainframe, although whether the system would be considered simply a single city or an entire "planet" (possibly both) is unclear.
• The Bad Guy Wins: The Web creature successfully opens a portal to the Web over Mainframe, leaving the system open for invasion.
• Big "NO!": Bob yells this when the Web creature turns the tear created by the Guardians' explosive into a portal to the Web.
• Cliffhanger: The Web creature opens a portal that will allow countless others of its kind to enter Mainframe. Bob tells Phong to prepare for war.
• Conspiracy Theorist: Fax Modem to a tee. In addition to his claims about Mouse, he insists that there is no User, and that Guardians send Game Cubes to promote the myth as a form of control.
• The Cuckoolander Was Right: Fax Modem is a dyed-in-the-wool Conspiracy Theorist whose sanity Bob openly questions, but he turns out to be right about the existence of the Web, and since his description matches the creature in this episode, it's likely that his sister really was abducted by a Web creature.
• Disconnected by Death: At first, it seems to those in Mainframe that Bob was deleted in the explosion of the Guardians' bomb, but eventually he manages to get through and explain that it was simply interference.
• Double-Meaning Title: "Trust No One". Is it referring to Turbo? That Mouse shouldn't have trusted him? Or even that the rest of the High Command shouldn't have left Turbo alone (to break protocol by giving Bob more time to get rid of the bomb)?
• Eldritch Location: The supersized tear created by the Guardians' bomb gets stabilized into a portal to the Web, which appears to be one of these, and now since Hyperspace Is a Scary Place, its denizens are poised to invade Mainframe.
• Entertainingly Wrong: Based on her fangs (coming from a childhood memory of Modem's sister's abduction) and her presence at the scene of multiple attacks, Modem and Nully theorize that Mouse is the Web creature in disguise; in reality, the fangs are a coincidence (indeed, compared to the real Web creature, Mouse's fangs are positively tiny), and Mouse has been tracking the creature, explaining why she's been seen near abduction sites.
• Final Solution: This is the Guardians' strategy of dealing with Web creatures. Rather than save a system that the creature's in, they destroy it completely to remove the possibility of the creature invading the rest of the Net.
• Godzilla Threshold: The possibility of a web creature creating a portal from the web to the net is treated as a potentially apocalyptic event, so if the Guardians have confirmation a web creature is in a system their protocol is to destroy it.
• It's the Only Way to Be Sure: The Guardians are more than willing to trade one system for the safety of the entire Net.
  Bob: Do you know what the Guardian protocol is for finding a Web creature in a system like Mainframe?
  Mouse: They have no intention of savin' us?
  Bob: They have every intention of destroying us!
• Nice Job Breaking It, Hero!: The bomb's explosion, though it occurs a safe distance away from Mainframe, creates a tear that the creature turns into a portal to the Web.
• Not What It Looks Like: Mouse gets temporarily suspected of being a Web creature, as evidence links her to the scene of every abduction. When Mike is attacked, Bob and the agents find Mouse standing over him; she insists this isn't what it looks like. We later learn she isn't a Web creature after all; she just drove the one attacking Mike away, and has been seeking evidence of the creature's presence on Turbo and the Guardians' behalf.
• Offscreen Villain Dark Matter: In a sense; the Web creature got huge relative to its last appearance, feeding off the combined energy of around a dozen sprites, binomes and numerals to bring it to a status where it is capable of stabilizing tears into portals, as it does at the end of the episode.
• Oh, Crap!: Bob is appropriately horrified to learn that Mouse alerted the Guardians about the Web creature; unlike Mouse, Bob is fully aware that Guardian protocol for such a situation is to destroy the entire system.
• The Omniscient Council of Vagueness: The Guardians in the Supercomputer are portrayed this way, with in backlit shadows. Prime Guardian Turbo obviously has a unique character design but is not seen in full until the next season.
• Real After All: Despite Bob's doubts, Fax Modem claims a strange creature with fangs abducted his sister. When the group hear the Web creature attacking Mike, Fax says that was the exact same noise made by the monster he saw in his youth.
  Modem: You see, Nully? The Web is out there.
  Nully: No, Modem, it's here.
• Relocating the Explosion: Once Bob realizes that the Guardians have left a bomb to destroy Mainframe, he wastes no time in trying to get it to safety, which is a big task given that the bomb is designed to destroy all of the system.
• Request for Privacy: After the Guardian High Command choose to destroy Mainframe to prevent the Web creature from spreading to the Super Computer, Turbo asks to be left alone with his thoughts. With everyone gone, Turbo then purposely increases the bomb's countdown to give Bob more time to find his own solution.
  Turbo: I'd like to be alone for this. Bob and I go back a long way. (Alone, Turbo flips the hourglass countdown) That's the best I can do. Good luck, Bob. I'm so sorry.
• The Reveal: Mouse is working for the Guardians; it's implied that she was close to Mainframe in "Gigabyte" because they'd already dispatched her to investigate the Web creature when it entered the system in "Nullzilla".
• Right for the Wrong Reasons: Modem's dead wrong about the origins of the Games and the existence of the User, but he's right that the Guardians aren't totally trustworthy; rather than try and save Mainframe from the Web creature when they learn of it, their plan is to destroy the entire system.
• Shout-Out:
  • Fax Modem and Data Nully are deliberate expies of Agents Mulder and Scully from The X-Files. Nully is even voiced by Gillian Anderson herself, who portrays Scully.
  • The Web Creature abducting people and putting them in a nest with sacks around them is similar to various horror films like The Thing (1982) and Alien.
• Skewed Priorities: After nearly being abducted by the Web creature, Mike's only concern is if the camera was still rolling.
• Two-Keyed Lock: All members of the Guardian High Command appear to have to activate their own switches in unison in order to activate the bomb that will destroy Mainframe. Not that they hesitate, however.
• Unwitting Pawn: Mouse worked with the Guardians to find a Web creature, but it turns out her communicator had a bomb installed in the event that the Guardians decided to destroy Mainframe to get the creature.
• Voice with an Internet Connection: Turbo, the leader of the Guardians, acts as one of these for Mouse as she seeks proof of the Web creature on his behalf.
• Weakened by the Light: Light causes the Web creature to go into stasis. However, even that is useless when it senses the massive tear created by the explosion, and it escapes to turn it into a portal and go home.
• Wham Episode: While there was something of an ongoing story since "Painted Windows," the creation of the giant portal to the web indicates the next episode will be all-out war.
• Wham Line:
  • Bob telling Mouse that the Guardian’s protocol is to destroy any system containing a Web Creature.
  • With a giant portal to the web in the sky, Bob calls Phong and tells him to prepare for war.
• What You Are in the Dark: Even after the Guardian High Command choose to destroy Mainframe, Turbo purposely increases the bomb's countdown to give Bob more time to find his own solution to the crisis.