In the first segment, Brain uses an enlarging ray to make himself and Pinky bigger. He dresses Pinky as Gollyzilla and has him terrorize the city with the plan to come in and save the city, however, he ends up fighting the Real Gollyzilla. In the second segment, Brain makes Pinky Smarter so he won't get in the way so much. In the final segment Brain sings a song to the tune of "Camptown Races" that goes over the different parts of the Brain.
Knowing that the population craves an honest politician, Pinky and The Brain mechanize the Lincoln Memorial and drive it around town, convincing the population that it's the reincarnated Lincoln. They meet with some success--but not quite enough.
Pinky arrives in Vienna circa 1946 to search for his friend, The Brain. Several people tell him that The Brain was killed in a chemical explosion. It is later revealed that The Brain is alive, but faked his death in the hopes of starting a new life.
Loved by the citizens of the country, Pinky runs for president with The Brain running as his vice president. The plan is working until The Brain's instruction book on world domination is stolen and he is impeached.
Animal rights activist think Pink and the Brain are monkeys and release them into the jungle after taking them out of Acme Labs. The pair try to make it back home, but run into the Brain's old enemy Snowball.
In "A LITTLE OFF THE TOP," Brain tries to discover the source of Samson's strength. In "MEGALOMANIACS ANONYMOUS," Brain joins a support group for those obsessed with the notion of taking over the world.
In "TWO MICE AND A BABY," a spoof of the Superman story, Brain and Pinky care for a boy with special powers sent to Earth by his parents. In "THE MAZE," Lab scientists use a chip critical to Brain's plan and he must get through a virtual reality maze to get it back.
The Pinky and The Brain who live in the future travel back in time to give their present-dwelling counterparts a book on how to take over the world. The present pair travel to the future and find themselves in a world where cockroaches and are ruling the planet. After being captured, they escape to their capsule, which takes them safely back to the lab. But when Pinky leaves the book in the capsule, the craft vanishes, leaving the jet-lagged mice pondering how to take over the world yet again.
Pinky and The Brain team with basketball coach Bobby Nacht and a crew of has-been TV actors to create the best squad in the NBA. With the aid of a mechanical arm and 3-foot-high shoes, The Brain soon achieves the kind of celebrity that he has always dreamed about. But just when The Brain is famous enough to contemplate taking over the world, his unchecked ego keeps him from achieving his lifelong goal.
The Brain enlists the help of beavers in his latest plan to take over the world by flooding it. In return for damming the water, the beavers want gum, boots and shiny things. The Brain makes his first attempt at flooding a city, but the city is well equipped for thwarting the disaster. When the beavers take the shiny remote control The Brain uses to communicate with, Pinky and The Brain are left powerless. Pinky and The Brain try to capture the adoration of the world by becoming movie stars. Their plan backfires when the world considers them comedic geniuses. Attempting to change his image, The Brain releases a dramatic film, but the audience becomes bored and leaves the movie theater, sending the two mice back to the lab.
Pinky and The Brain's latest plans are hindered by the presence of their new, uninvited sidekick, Larry. In order to gain control of the steel industry, The Brain claims that he and Pinky are among the last of the nearly extinct Mousealope species, whose natural habitat is Pittsburgh.
The Brain, disguised as famous actress-singer Cher, enters a celebrity golf tournament in order to steal Chi Chi Rodriguez' putter, with which he intends to tattoo "Property of Brain" onto the Earth. But in a fit of competitive anger, The Brain breaks the putter across his knee, thus thwarting yet another plan to take over the world. When The Brain invents a machine that brings the Earth to life, the planet is so grateful that it grants The Brain his every wish. World leaders are forced to pledge their allegiance to The Brain or face the consequences of devastating natural disasters. But The Brain asks too much of the Earth, and the planet turns against him. Gentle Pinky finally convinces the Earth that killing is not in its nature, and the planet asks to return to its former, unconscious self.
Pinky and The Brain are forced to befriend their eccentric neighbor, Sultana, in order to retrieve an important package that he has accepted on their behalf. Posing as Mr. and Mrs. Feldman, the two lab mice visit Sultana's home and slowly win his confidence. Pinky and The Brain's kindness only increase Sultana's feelings of loneliness, however. Sultana tries to end his life by climbing a radio tower in an electrical storm. The Brain, who is actually trying to save the entire planet from being electrocuted, inadvertently saves him. Sultana's promises of eternal gratitude may force the two mice to search for a new apartment.
In "All You Need is Narf" it is the 1960s and Pinky becomes a guru. Pinky unites a member of the most popular band of the day, a parody of the Beatles, to his true love causing the band to split up. In Pinky's plan, it is Brain's birthday and he realizes he is getting old so he takes the day off. Pinky plans on throwing Brain a party at "Chuncky Cheeses" with all the world leaders. Pinky's gift to Brain, the World, but Brain in his selfishness manages to screw it up.
While reading a book to learn from the mistakes of great leaders of the past, The Brain leads Pinky on a whirlwind tour of history in this musical cartoon. Included are profiles of Cleopatra, Caligula, Hannibal and Napoleon. To carry out The Brain's latest plan, he and Pinky go undercover among the Minnesota Rhennish, a strict rural community that eschews modern technology and buttons. Unfortunately, his scheme is interrupted by frequent barn construction.
After being stalked by a conspiracy theorist-filmmaker, Brain decides to take advantage of conspiracy theories by creating one about himself that claims the government is keeping Brain from stepping into power.
In the 1930s, The Brain notes the popularity of tap dance and constructs a pair of steam-powered legs to send a subtle Morse code message of world domination. Bereft of ideas to take over the world, The Brain travels to Hollywood to get plots from screenwriters.
The Brain uses a dance to demonstrate the true poetic majesty of world domination in this musical interlude. The Brain becomes a fashion designer and Pinky becomes a supermodel to promote a mind-controlling fragrance.
In a horrible lab mishap, Pinky becomes a really suave guy. The Brain and Pinky infiltrate a secret organization of world leaders, where they must endure humiliating initiation rites to succeed in their latest scheme.
In the early 1960's, The Brain opens a resort in Las Vegas to finance a plan and poses as a singing star to draw patrons. In the process, he becomes an ultra-cool icon and the leader of the celebrated Mouse Pack.
Discovering that the best way to take over the world is through pacifism, Pinky and The Brain travel to the Southwest on horseback and create a colony to teach the world the value of peace, love and improvisation.
Brain tries to hypnotize Sigmund Freud, but Pinky accidentally leaves Brain's mirrored glasses behind. Then, Pinky and the Brain travel to Japan so Brain can become a sumo wrestler to obtain a rare Japanese fish as part of his latest plan.
In this song segment, Pinky and The Brain are the pets of a crazy tailor. While the lab is closed for summer vacation, The Brain plans to travel to Camp Davey, the lodge for children of dignitaries who are visiting Camp David. Once there, his goal is to become crafts counselor and have the children make wooden pencil holders in which he will plant listening devices, enabling him to hear the conversations of global leaders and create a better plan to take over the world. But first, he and Pinky must ascend to the senior counselor position by eliminating all the other counselors above them.
During a White House conference on the topic "the brain," one of the president's assistants mistakenly invites The Brain. After he becomes trapped in a web of conspiracy and deception, The Brain gets brainwashed and Pinky must save him.
To facilitate The Brain's latest plan, he and Pinky ship themselves to Russia, where they become involved in a James Bond-style adventure. Pinky and The Brain find themselves trapped in the familiar nursery rhyme.