Wendy and Tyler are leaving a coffee house where Tyler performed… and Wendy was his only audience. Tyler is cool with it and confident he gave a great performance. They stop off for hot dogs at a street stand and Wendy starts rambling to the stand owner while two cars crash in the intersection behind them. One driver pulls out a baseball bat and prepares to attack the other, and Tyler quickly disarms him. The victim, a richly-dressed man, praises Tyler on his diplomatic skills and physical skills, and offers him a job. He gives Tyler his card and departs.
The next morning at the sublet, Tyler comes down from Wendy's room for breakfast while Wendy gets a two-minute emergency alert from The Middleman, who warns they have a nine pan-galactic incursion. Tyler shows Lacey and Noser the man's card and they recognize him as Manservant Neville, owner of Fatboy Industries and creator of the uMaster portable green-friendly music system that everybody owns. They're interrupted when The Middleman arrives in a hazmat suit. As they leave, he explains that Voyager 2 is heading back to Earth despite the fact it was sent on a one-way trip out of the solar system.
The duo arrives at Voyager 2's crash site and recover the black box. A team arrives and The Middleman identifies himself and Wendy as NASA scientists. The new arrivals are NASA, but The Middleman quickly intimidates them into backing down. They take Voyager's black box back to Middleman HQ.
Lacey and Noser listen to Tyler's newest song and congratulate him on his talent. Manservant Neville arrives and knows all about them. He insists that fate has brought them together and wants Tyler to work for him. He tells Tyler to come to Fatboy Tower the next day and then departs. Lacey insists that Tyler goes and she'll drive him.
The Interrodroid 5000 brings in the Voyager black box into Ops. They open it and find a metal item with Clotharian glyphs on it. Wendy remembers Clothar as the galaxy that sent five dictators to Earth where they formed Varsity Fanclub. The item detonates, destroying Interrodroid 5000 and releasing a virus setting off an alert that seals off the entire HQ. Ida gets Wendy and The Middleman into decontamination as they disrobe. The Middleman asks for some privacy and then informs Wendy that they have to remove all of their clothing and scrub down.
Lacey and Tyler arrive at Fatboy Tower and have to wait. Lacey assures him he's going on an adventure and the worst that can happen is that he turns down Manservant Neville yet again. Tyler is called away and informed that he'll have to take a few tests. Tyler undergoes a series of bizarre mental and physical tests.
Wendy and The Middleman finish their d-con procedure and Ida informs them that she's still developing the cultures. The Middleman suggests she contact the Clotharians and find out what's going on. While they wait, The Middleman explains that a Code 47 is necessary: pre-recorded messages a Middleman makes if they anticipate dying. He plays back several of his prerecorded missions for her. Wendy refuses to make a Code 47, noting that her friends knowing everything about her and she has nothing to say to them. The Middleman records a new message for Wendy, who reminds him that she's in the room. Since the corridors should be contaminated, they contact Ida on the security monitors. She appears inactive and they realize the tape is looped and Ida has been compromised. The Middleman activates the Nakatomi Emergency Protocol, which enlarges the air ducts to a navigable and shuts down the interior sensors. They crawl to Ops and see Interrodroid 6000 using HEYDAR to turn Ida into a walking detonator destroying the entire city in 60 minutes. Ida hears them talking in the vents and orders the Interrodroid 6000 to kill them. They leave the vents and get to the changing room where Wendy acts as bait so The Middleman can rip off the robot's head. The Middleman concludes the virus targeted Ida and they're immune, and comes up with a plan using the Interrodroid's severed head.
Tyler is brought before the board of directors of Fatboy Industries. The head CEO ruthlessly interrogates him about all of his flaws and poor decisions. Tyler defends himself and then notices that the CEO can't pronounce Manservant's name correctly. He identifies other flaws in the board members and realizes that they're all part of one final test of his powers of observation. The proctor arrives and escorts Tyler out.
The Middleman hooks the Interrodroid's head into the phone system and draws upon its memories of the previous Interrodroid to contact the Clotharian High Aldwin. He suggests Wendy make a Code 47 but she refuses. They contact Aldwin, who is now Maximum Aldwin. The Middleman invokes the Perpugilliam Treaty to force Aldwin to explain why he's having them killed. Aldwin informs them that Voyager 2 came through a wormhole and started photographing a secret military base. They send back a payload of nanobots to infiltrate Earth technology and rip it apart from the inside out. The explosion will spread the nanobots across the planet and reduce mankind to Stone Age technology.
Aldwin cuts the transmission and The Middleman suggests they deactivate Ida using her reset switch, which will stop the explosion. However, any attack will set off the explosion prematurely. He proposes using the HEYDAR's shrink ray to reduce him to microscopic and use its particle accelerator to shoot him into Ida'a brain where he'll go to her cortex chamber and hit the reset switch. However, Ida is hooked up to HEYDAR. Fortunately, there's a Baby HEYDAR. Wendy dresses up as the Interrodroid and goes into Ops, and stumbles around to create a distraction. The Middleman drops into Ops to take the Baby HEYDAR but they're interrupted when the new Interrodroid 7000 arrives. The two Interrodroids accuse each other of being a fake. Ida shoots the new arrival first and then prepares to kill Ida. The Middleman shoots the HEYDAR connector, dropping it on Ida. They get out the door but Ida gets the drop on her. The Middleman is forced to shrink Wendy and then shoot her into Ida's sinus cavity. She heads for the brain while The Middleman tries to stay one step ahead of Ida. He explains that it's crucial that she get out of Ida's body when she hits the reset switch. If she's inside Ida when enlarged, she'll be shredded.
Wendy spots the nanobots working inside of Ida's body. The Middleman warns that they're indestructible and attack in swarms, and advises Wendy to evade them.
Tyler is preparing to leave when Manservant Neville arrives but is astonished that Tyler is turning down his offer. Neville notes that the world crushes those with talent and he's offering Tyler the chance to change the world. He needs a right hand man, someone with music in their soul.
With 17 minutes left, Wendy gets to the hatch to Ida's cerebral cortex. The Middleman tells her to outsmart them. Ida finds him and warns that no matter what he does, she'll explode sooner or later and spread the nanobots. The Middleman manages to disarm Ida and wrap her up in chains. Inside of Ida, Wendy draws off the nanobots and slips into the cortex chamber. A diplomatic well-dressed Ida greets her: the representation of Ida's brain. They have five minutes left but Ida warns her that the nanobots have already trashed the reset switch. Ida has a new suggestion: send her back to OS2TK and they'll wipe her body of the virus. Ida knows how to send faulty equipment back and Wendy realizes there's an access point in Middleman HQ.
The Middleman brings Ida's body to Ops with three minutes left. Ida's brain instructs him in how to open a secret panel to reveal a pneumatic tube. The Middleman places Ida's body in the tube but the nanobots start to break in to the cortex chamber. Ida explains that if Wendy is sent back inside of Ida's body, OS2TK will dispose of her for good.
With time running out, Wendy insists that The Middleman send her back and sends her own Code 47 to him. She thanks him for being a father figure to her since her own father disappeared, and giving her the chance to be his sidekick. He tells her never to give up and she remembers the nanobots are indestructible. She lets the nanobots in and tells The Middleman to enlarge her. The nanobots come in and advance on Wendy, who gives the order to The Middleman to enlarge her. Wendy explodes out… protected by the enlarging nanobots' indestructible body. The Middleman sends Ida's body on to OS2TK with seconds to spare and the lockdown ends. The nanobots are harmless with no technology to enter from the inside to dismantle. Wendy asserts that everything that she said, she meant.
Later, Wendy meets with Tyler and discovers he's wearing a suit and has taken a job as Manservant Neville's assistant. They stroll away, happy. At Middleman HQ, The Middleman tries to open the panel again and discovers the pneumatic tube is now gone. The new Ida arrives, back to her old self, and The Middleman wishes her a good night.