After a team told HQ the location and passphrase for Moriarty's lair, they were instructed to show up outside the 26-5 elevator. In the elevator, an E.I.T. receptionist waited behind a desk. She verified that they were authentic S.P.I.E.S. agents by asking questions whose answers were puzzle answers from the Brain's round.
The receptionist then started the descent down into the earth (one floor!) and sent the team to the 26-4 women's bathroom, informing them that Dr. Honey Bare was unconscious within, having been caught and drugged by E.I.T. agents. Remembering what James Bond had told them, they woke her up with some music by the incomparable Barry White. She ascertained that they were good guys by asking questions that yielded answers from James Bond's round.
Dr. Honey Bare next gave the team a page (PDF) with an irregular grid of letters and numbers on it. Laying the spatula that the Swedish Chef had given them on the page so that the top and bottom row of holes in the spatula all covered shaded cells in the grid, it was possible to read the phrase EIT CENTRAL SERVER and a telephone number. When they called that number, the E.I.T. Central Server dude who answered wouldn't speak to them until they demonstrated their trustworthiness by answering a question from the Swedish Chef's round.
The server dude gave Dr. Honey Bare directions to the Central Server room, and she led them there. Unfortunately, the only path from 26-4 to the server room happened to pass through 34-302, which contained Moriarty's EITMaster 9000 bomb — armed, dangerous, and counting down. Fortunately Natasha Fatale had given the team the plans (PDF) for the bomb, with the aid of which it was possible to deactivate the bomb. (Unfortunately, no team was able to disable the bomb on first try; when a bomb blew up, teams had to run and find a new route to the center of the earth, complete with "new" bomb.) That disaster averted, the team proceeded to the server room in 14-0637. The server dude asked them questions to elicit puzzle answers from Natasha's round before letting them in.
Once in the server room, the team had access to the E.I.T. Central Server: a single laptop which was, at the time, running a game of Nethack. After using the intelligence shared by Dana Scully to win the Nethack game, the team successfully logged on to the E.I.T. Central Server and received a message from root. After making them confirm a puzzle answer from Dana Scully's round, root advised them to investigate Moriarty's interrogation records in 36-372.
The door to 36-372 was guarded by E.I.T. agents. Remembering Stewie Griffin's advice, the team found that behaving like cheerleaders would distract the agents long enough to allow them to enter the interrogation record room. Moriarty's interrogation records were filed in a confusing system in one folder, but, aided by the team's knowledge of puzzle answers from Stewie Griffin's round, Dr. Honey Bare was able to find the document they needed.
This document was a list of descriptions of S.P.I.E.S. agents that E.I.T. had interrogated. The team used the information shared by Rosencrantz & Guildenstern to solve this puzzle and learn the name of a S.P.I.E.S. agent being held prisoner in Moriarty's dungeon. Dr. Honey Bare led the team to that agent's cell in the basement of Building 4, where he refused to speak with them until they answered a question about a puzzle answer from Rosencrantz & Guildenstern's round.
Once he was satisfied of their identity, the imprisoned agent informed the team that Moriarty was at that very moment about to activate his Evil Weather Machine in the subbasement of Building 9, under the mural of a giant ship! The team rushed there and found Moriarty himself himself awaiting them there. He challenged them to the ultimate battle of wits: a game of "What Number Am I Thinking Of?" He would have won, too, had not Inspector Gadget already alerted the team to the fact that Moriarty cheats, and told them exactly how. Though he had been outwitted, however, Moriarty boasted that his machine had already been activated, and fled to go skiing in Hawaii. But one of his bodyguards realized: "I hate skiing!" He overpowered the other bodyguard, and — after asking the team questions about answers from Inspector Gadget's round — gave them a document.
The document turned out to be the top secret directions to the heart of the weather machine, which the team decoded by remembering that Ethan Hunt had told them of Moriarty's affinity for the first book of Kings in the King James Bible. They followed the directions and traced out the route to the central core of the weather machine.
When teams reached the core in the basement of Building E18, though, they found a note from an E.I.T technician saying "It's so hot in the center of the earth that our vital part kept melting. I've managed to put it somewhere safer nearby that is close enough to the machine." The "safer location" turned out to be a nearby row of refrigerators; the vital part of the weather machine — and the coin of the 2006 Mystery Hunt — was the snowglobe hidden inside one of them.