A man observes a mysterious glass box, South Dakota police discover a hideous crime and Hawk receives a cryptic message about Special Agent Dale Cooper.
Dale Cooper remains trapped in the Black Lodge. In Twin Peaks, Dr. Jacoby receives a shipment of shovels. At the Great Northern, Ben Horne introduces his brother Jerry to his new secretary, Beverly. Deputy Chief Hawk gets a call from the Log Lady, who tells him some evidence relating to Dale Cooper is missing.
In New York City, Sam Colby sits in a warehouse watching a glass box. Tracey Barberato visits him. With the security guard absent during Tracey's second visit, Sam lets her into the room. As they have sex, a pale androgynous entity--the Experiment--materializes in the glass box and murders them.
In Buckhorn, South Dakota, Cooper's doppelgänger--a sinister, long-haired man with black irises--retrieves two associates, Ray and Darya. Police find the severed head of Buckhorn librarian Ruth Davenport placed on the headless body of a John Doe. Local principal Bill Hastings's fingerprints are found and he is arrested. Bill denies guilt, but fumbles his alibi.