In order to obtain all the world's money, Brain must reprogram a satellite orbiting the Earth. Luckily, NASA is offering the opportunity for one child to go on the next space shuttle mission. Pinky and The Brain have the enormous task of teaching Elmyra about the solar system in order for her to win the trip.
A vicious cat prevents Pinky and The Brain from carrying out their world domination plans. To make the cat more obedient like a dog, Brain concocts a DNA cocktail, but the cat's personality is altered in a way the two mice didn't expect.
Pinky and The Brain pose as reporters in an attempt to make Elmyra popular. According to The Brain's theory, being popular should give her more friends, giving Pinky and The Brain more time to take over the planet.
Pinky and The Brain build a clubhouse where children can gather without being hassled by adults. The Brain desires to use their unhappiness with society as a launching point for a revolution. But Elmyra and the kids have other plans.
Rudy inadvertently alerts a mysterious group called The Circle that is pursuing Pinky and The Brain. Soon, an agent of The Circle, Wally, pursues the two mice.
Elmyra writes a paper about her weekend which involved a trip to Paris with Pinky and the Brain. Brain's plan was to take over France, and if th people would not submit he threatened to turn all their cheese into stupid American tourists.
In a parody of Frank Capra's classic holiday film, "It's A Wonderful Life," The Brain dreams that he is back at Acme Labs. He soon learns what existence would be like if Elmyra replaced Pinky.
The Brain invents a powerful scent that draws people to whoever wears it. But Elmyra inadvertently takes the scent to her school dance. The Brain must now infiltrate the event in his Patty Ann suit and retrieve the concoction.
Pinky becomes enamored with the vision of a perfect life displayed by 1950s television comedies. After Elmyra buys Pinky a 1950s-style dollhouse, The Brain is slowly drawn into Pinky's fantasy world.
Pinky and The Brain become Elmyra's campaign managers after she is nominated for class president. However, politics proves tricky, as they must manipulate Rudy Mookich into opposing Elmyra's opponents.
After the annoying theme song from a children's amusement park ride is ingrained in their minds, Pinky and The Brain decide to alter the tune for their purposes. But in order to do so, they must negotiate the world's most chaotic theme park, Duckyland.
A teleportation device goes awry, fusing The Brain and Elmyra into a two-headed being. Captured by a sinister carnival owner, their rescue is in Pinky's hands.
Pinky and The Brain broadcast their world domination plans on a public access TV station. However, when network executives accidentally see the show, they decide to air it nationally.
Elmyra takes Pinky and The Brain and several other pets to the veterinarian's office. When the doctor wants to publicize her bizarre cat/dog, Pussy Wussy, the mice must act to prevent discovery by The Circle.
After learning that Rudy won't attend Vanity's big party, Elmyra begins sobbing uncontrollably. To stop her crying, Pinky and The Brain use the Patty Ann suit to lure Rudy to the event.
Pinky and The Brain attempt to win public support by faking crimes and having The Brain, in the guise of crimefighting hero Braino, foil them. However, their plans backfire when Elmyra begins to gain fame as crimefighting hero Underwear Head.
