Episode 1
Pinky and Brain are kidnapped in Washington, DC by an unknown force. Brain loses his memory and the mice are then imprisoned in a town where everyone is forced to perform the Schëerskåhøvên, which is dumbing down the entire country.
Episode 2
Brain regains his memory and the mice escape. They believe Snowball is responsible for the Schmëerskåhøvên, but him imprisoned in a mental institution.
Episode 3
The mice and Snowball search for the one who spliced their DNA, Dr. Mordough, thinking he's responsible for all this. But it turns out to be his cat, Precious, and time is running out.
Episode 4
Pinky and Brain's plan to alter caviar with a mutating capsule is complicated by a Russian lab mouse.
Episode 5
Brain plots to make every clock on Earth chime repeatedly.
Episode 6
A special of highlights of their career is on the air, but it's really all a ruse so Pinky and Brain can hypnotize the viewers.
Episode 7
Inspired by legends of the past, Brain tries to create a legend about himself to gain world acclaim.
Episode 8
How Acme Labs became home to Pinky and Brain.
Episode 9
In the series finale of Pinky and the Brain, the Brain, and the characters from Animaniacs develop a Star Wars spoof.