On a barren plain, a man staggers along and remembers how Dr. Jonas Venture stranded him there 30 years ago. A massive black portal opens in front of him.
At the Venture compound, Dr. Venture is working with Brock, bringing out his father's old machine. He ends up going into a hole. He finds himself in an underground tunnel, part of a long-abandoned complex. He's unable to contact Brock on his wrist phone. Brock goes downstairs and opens a secured door… and the man from earlier, only a few inches tall, attacks him. Brock kicks him away and comes in, inadvertently sealing the door behind him. The man demands to know where Dr. Jonas Venture is but then the door seals behind them, with a time lock set for 40 years.
Hank and Dean go to Dr. Orpheus, an expert in people vanishing into thin air. Orpheus agrees to help and prepares to assemble the Order of the Triad using action figures.
Brock is trying to break out while the man explains that he was stranded there during an experiment gone awry, and has been there for 30 years battling ants. The system broke down and Jonas abandoned him there.
Orpheus contacts the Alchemist and Jefferson simultaneously, and things get confusing since they can't tell which one of them he's talking to. Jefferson is apparently in London, and Orpheus is angry that Jefferson has left town, only to reveal that he's in an amusement park exhibition. Orpheus teleports his fellow Triad members to his home at the Venture compound, where they're duly impressed with his work on the action figures.
Dr. Venture is exploring the tunnels as a figure moves in the background behind him. The man then appears before him, dressed in a red-white-and-blue shirt.
The Triad go over the drilling machine and the boys wonder if they're in the basement.
Brock chats with Dr. Paul Entman, who explains he used to be 15' tall but Jonas tried to find a cure and shrunk him instead. Meanwhile, the Triad enter into the tunnels and Orpheus tries to get a psychic link.
Brock tries to remember which Marvel hero Entman reminds him of, while the Triad join hands and sense an unearthly presence and run back to the surface in terror. Orpheus decides to seek guidance from the Master, although his teammates think Orpheus is embarrassed by them.
Dr. Venture runs through the tunnels until he finds an emergency phone. He picks it up and ends up talking to Brock. The mysterious figure is running around, claiming he's a firestarter. More figures appear, wielding weapons and wearing Young Rusty Venture t-shirts. They call each other Rusty and take him away in a monorail car and demand to know why they haven't seen him before. They say that it's forbidden to go up above but he offers to let them come up if they let him go. They consider it but decide to let Father decide.
Dr. Orpheus says he was told to call the equivalent of Tech Support: he found Pete White's phone number. Pete checks out all of the security monitors from the formerly-secret security base. He finds a tape of Brock but can't access the cameras in Entman's chamber. He tells the boys to plug in any loose cables and they find one leading to a socket labeled MUTHER.
Brock is discussing Entman's abilities, although he doesn't have much. They're interrupted when the super-computer, MUTHER, comes online and asks to speak with Jonas Venture. Entman warns that Jonas Venture built the computer to monitor the facility and it ruined Entman's life.
Orpheus brings food for Peter and the boys, and recognizes MUTHER as the evil presence. It says that if they can't put it in contact with Dr. Venture, it will launch nuclear missiles and starts to contact the Ven-Tech missile system… by antique modem.
The Rustys take Dr. Venture to their "Father," a programming bed, where the other members of their group are assembled. They play a recording card of Jonas, talking about personal hygiene in a post-nuclear world. The Rustys all mimic Jonas' demonstration until Dr. Venture pulls out the card. He tries to take over as their god and orders them all out, but they speak of contamination and overwhelm him.
Jefferson suggests that they go directly after the bad guys and the Triad joins forces, while Entmam explains to Brock that Jonas used mood-enhancing drugs pumped into the atmosphere to keep happy the settlers of his post-nuclear underground base. MUTHER disagreed and bumped high doses of hallucinogenic drugs into the compound when Jonas and Team Venture were giving a tour. Jonas and his Team Venture barely managed to escape in the drilling machine, leaving the others on the tour behind.
Jefferson leads them to the drilling machine and they head down into the complex. Meanwhile, Dr. Venture is fleeing from the family and finds himself hanging from a nuclear missile. MUTHER detects a WOMB breach as the drilling machine arrives, and makes a full nuclear commitment.
Dr. Venture climbs to the top of the rocket and… it launches. Pete and the boys look on as they prepare for a holocaust, but the missile falls over and spills out all of the Rustys' excrement. Dr. Venture is left to crawl in the fluids. Later, Rusty explains that the Rustys were all Honorary Gold Members of the Rusty Venture Fan Club. orphans that Jonas gave them a tour of his state-of-the-art fallout. Since then, their only contact has been Jonas' recording and VH-1. Meanwhile, Brock and Entman plug in the recording card into MUTHER's computer and leave her to "talk" to him about personal hygiene.