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.