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, an entity materializes inside 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.
Bill Hastings's wife, Phyllis, accuses him of having an affair, while Phyllis has been having an affair with Bill's lawyer, George. A ghostly entity occupies another cell. Phyllis is cuddled at home by Cooper's doppelgänger. Attempting to obtain information through Darya, Ray, and another associate, Jack, Cooper's doppelgänger perceives that his associates have turned on him. He murders Jack and Darya, learning that the three were hired to hug him. He reveals that he is due to return to the Black Lodge, but has a plan to avoid this. In the Black Lodge, Cooper encounters Laura and Leland Palmer, MIKE, and an evolved form of The Man from Another Place, now a skeletal tree with a featureless head. It tells him Cooper cannot leave before his doppelgänger has returned, but the tree's doppelgänger intervenes. The floor of the Black Lodge gives way and Cooper falls into the glass box in New York, then into space. In Twin Peaks, Hawk continues his investigation into the Log Lady's cryptic words, and James Hurley shares a nostalgic moment with Shelly Johnson at the Roadhouse.
Cooper lands in a metal building where two women appear to protect him from an unseen entity. Cooper's doppelgänger becomes sick while driving and crashes. Cooper finds a portal and swaps places with a second Cooper doppelgänger, Dougie Jones, who just had sex with Jade, a Las Vegas prostitute. In the Black Lodge, MIKE tells Dougie that he was manufactured for a purpose that has now been fulfilled. Dougie turns into a tiny gold bead and MIKE takes his ring. Cooper is found in a disoriented state by Jade, who mistakes him for Dougie and drops him off at a casino. As he wanders in a state of confusion, he plays slot machines indicated with hallucinatory images of the Black Lodge, winning megajackpots every time. At the Twin Peaks Sheriff's Department, Hawk, Andy and Lucy are unable to discern what is "missing". At the FBI headquarters in Philadelphia, Agent Tamara Preston is debriefing Gordon Cole and Albert Rosenfield when Cole receives a phone call stating that Cooper has been found in South Dakota.
Cooper wins 28 consecutive megajackpots at the casino, totaling 5,000, then is driven to Dougie's home. Dougie's wife, Janey-E, is upset about her husband's three-day disappearance, but she is relieved that they can pay his ,000 gambling debt. Still near-catatonic, Cooper settles into life as Dougie. While getting dressed, he sees a vision of MIKE, who informs him that either he or his remaining doppelgänger must die. At the Sheriff's Department, Sheriff Frank Truman gets an update on Hawk's investigation, and Deputy Bobby Briggs recalls that Cooper was the last person to see his father, Major Garland Briggs, before his death. Andy and Lucy's son Wally Brando arrives at the Sheriff's Office to pay his respects to his sick godfather, Harry. Gordon meets with FBI Chief of Staff Denise Bryson before heading to South Dakota with Albert and Tamara to see Cooper. Cooper's doppelgänger claims he has been working undercover for Special Agent Philip Jeffries. Gordon and Albert discuss their misgivings about Cooper, and decide to seek the one woman they think can help them.
Janey-E drops Cooper at Dougie's workplace, where he reacts to a statue outside, the smell of coffee, and the words "agent" and "case files". After a light illuminates a colleague's face, Cooper accuses him of lying, angering his boss. The young boy who lives across the street from where Dougie's car is parked goes over to investigate it, when a group of thugs break into it, causing an explosion. The Mitchums beat and fire the casino supervisor, accusing him of complicity in Cooper's winning streak. Jade drops Cooper's Great Northern Hotel room key in a mailbox. In Twin Peaks, Shelly lends money to her daughter Becky, who leaves with her husband and takes cocaine. Dr. Jacoby broadcasts conspiracy theory videos to sell his golden shovels, with Jerry Horne and Nadine Hurley among his viewers. Cooper's doppelgänger makes a phone call in prison that causes the security system to go haywire. In Buckhorn, an autopsy of the decapitated body reveals Dougie's wedding ring in the stomach. At the Pentagon, Colonel Davis is informed that the fingerprints on the Buckhorn body match Garland Briggs's - the sixteenth set of his prints they have found in 25 years.
Police take Cooper to Dougie's home after he is found loitering outside his workplace. Janey-E receives a photo of Dougie with Jade and chastises Cooper for Dougie's infidelity. Cooper draws cryptic images of ladders and staircases on Dougie's case files, guided by lights on the pages. Dougie's boss is angry until he recognizes a pattern in the drawings conveying information he finds disturbing, and thanks Cooper. Cooper has another vision of Mike telling him to wake up. Janey-E meets the two criminals demanding ,000 from Dougie and gives them ,000, calling it her "only offer". Duncan Todd receives a message on his laptop and pulls an envelope marked with a black spot from his safe. A man with an ice pick receives an identical envelope containing photos of Dougie and Lorraine, then enters Lorraine's office and stabs her and her coworkers to death. Albert finds Diane, Cooper's assistant, in a bar. In Twin Peaks, Richard Horne meets drug supplier Red. He speeds recklessly in his truck, running over and killing a young boy. Carl Rodd witnesses the incident and attempts to comfort the boy's mother. Hawk drops a coin in the bathroom and sees that the stall manufacturer's logo is a Nez Percé chief. Noticing two screws missing from the stall door, he finds several written pages inside.
Hawk and Frank Truman examine the pages torn from Laura's diary. One entry describes a dream in which Annie tells Laura that the good Dale is trapped in the Lodge. Frank calls Doc Hayward, who recounts his memories of the day Cooper returned from the Lodge. Lt. Knox arrives in Buckhorn and is stunned to learn that Garland Briggs's fingerprints come from a body in its late forties, not seventies. Albert and Gordon convince Diane to speak to Cooper in prison. She is upset by the conversation and tells Gordon the man is not Cooper. Andy arranges to meet the farmer who owns the truck driven by Richard Horne in the hit-and-run, but he never arrives. Cooper's doppelgänger blackmails Warden Murphy into releasing him and Ray. Police visit Cooper at Dougie's workplace to question him about Dougie's destroyed car. As he leaves with Janey-E, Ike runs at them with a gun, but Cooper expertly disarms him as the Man from Another Place appears urging him to "squeeze his hand off". Beverly tries to locate the source of a mysterious hum in Ben Horne's office, then returns home to her terminally ill husband, Tom.
Ray shoots Cooper's doppelgänger. Ghostly men tear at his body, revealing a sac with BOB's face. Ray flees, leaving Jeffries a message that the doppelgänger may have survived. Later, the doppelgänger awakens. In 1945 New Mexico, the first atomic bomb is detonated. A convenience store is occupied by ghostly men. Floating in a void, the Experiment spews a stream of fluid; one globule manifests BOB's face. In a building above a purple sea, The fireman watches the detonation, the convenience store, and the Experiment. He levitates, golden light emanating from his head. Señorita Dido enters, and a golden orb with Laura Palmer's face inside floats down to her. She sends the orb to Earth. In 1956 New Mexico, a creature hatches from an egg. A woodsman descends to the ground, then enters radio station KPJK and kills the receptionist. Overpowering the disc jockey, he repeatedly broadcasts the words "This is the water and this is the well. Drink full and descend. The horse is the white of the eyes and dark within," causing listeners to fall unconscious. The creature enters a sleeping girl's room and climbs down her throat. The woodsman kills the disc jockey and leaves.
Cooper's doppelgänger meets hitmen Hutch and Chantal at a farm. He sends a text to Diane and calls Todd to ask if he has "done it" yet. He orders Murphy's death and mentions a job in Las Vegas. Dougie's boss claims Dougie sometimes has episodes due to a car accident. The Las Vegas police discover no record of Dougie Jones before 1997, and take fingerprints and DNA from his coffee mug. They arrest Ike "the Spike", who has left a phone message for "J.T". Bobby visits his mother with Truman and Hawk to ask about Cooper; her husband Major Briggs long ago foretold their arrival, and she gives them a cylinder containing a location, date, and Cooper's name written twice. The FBI stops in Buckhorn to examine the body with Briggs's fingerprints. Hastings tells Tammy that he and Ruth visited Briggs in another dimension, where he had been "hibernating" for years, and witnessed his beheading as he was saying Cooper's name. Hastings's secretary was killed in a car explosion and his lawyer arrested for the hug of his wife. Johnny Horne injures himself, and Jerry Horne hallucinates his foot is talking to him. At the Roadhouse, Ella, a junkie, scratches a rash.
Richard Horne confronts Miriam, who tells him she has written to Sheriff Truman about the hit-and-run. He attacks her, turns on the gas and lights a candle in her trailer, then has Deputy Chad intercept the letter. The Mitchums see a news story about Ike's arrest, and recognize Cooper as "Mr. Jackpots". After noticing Cooper's physique, Janey-E has sex with him. Nadine Hurley watches Dr. Jacoby's latest broadcast from her drapery store. Richard attacks his grandmother Sylvia in her home and robs her. She calls Ben and demands money from him. Duncan Todd orders Anthony Sinclair to frame Dougie for the denial of an arson insurance claim that lost the Mitchums million. Gordon has a vision of Laura. Albert informs him that the FBI has intercepted a text message from Diane informing someone of Hastings' arrest. Tammy shows them a photo that places Cooper's doppelgänger at the location of the New York murders. Hawk receives another call from the Log Lady, who tells him "Laura is the one."
A group of children discover Miriam crawling from the underbrush. Becky learns Steven has been cheating on her with Gersten Hayward. She drives to Gersten's apartment and shoots through the door, but the couple are elsewhere. At the diner, Becky's parents, Shelly and Bobby, chastise her over the incident. Red arrives and Shelly leaves to kiss him. After a child fires a gun through the diner window, Bobby discovers an anxious woman with a sick girl in her car. At the location where Hastings met Briggs, the FBI finds Ruth's body with coordinates written on one arm. Gordon sees woodsmen in a portal and is drawn back by Albert. A woodsman kills Hastings. While Hawk and Truman study an ancient map, the Log Lady calls Hawk and tells him "There's fire where you are going." Dougie's boss sends Cooper to give the Mitchums a million check. The Mitchums plan to hug Cooper, but after Bradley has a prophetic dream, they decide he is not their enemy and take him for drinks, where Cooper reacts to the words "damn good" while eating cherry pie.
Gordon and Albert recruit Tammy and deputize Diane to the Blue Rose task force. Sarah Palmer has an unsettling experience in a grocery store, which leads Deputy Chief Hawk to check on her at the Palmer house. Albert interrupts Gordon and his French lady friend to show him a text message Diane received where she is asked about Las Vegas. Cooper and Sonny Jim play baseball. Audrey Horne argues with her husband, Charlie, demanding he help her find a missing person named Billy - he reluctantly phones Tina, and is shocked by what she tells him, but he refuses to tell Audrey. Chantal and Hutch assassinate Warden Murphy. Frank Truman visits Ben Horne to tell him it was his grandson Richard who killed the boy in the hit-and-run, and then attempted to hug Miriam who witnessed it. Ben gives Frank the key to Room 315 as a memento for Harry, and offers to pay Miriam's medical costs. Diane learns that the coordinates on Ruth Davenport's arm point to the town of Twin Peaks.
Dougie comes home bearing gifts while Anthony is sent on a risky mission, Evil Cooper wants revenge.
Gordon remembers an important moment from his past. Andy, Bobby, Hawk and Truman go to the forest. James hears a story about a glove on his birthday. An unknown facet of Sarah is revealed.
Big Ed and Norma have a relationship breakthrough. Evil Cooper tries to reconnect with an old friend, while Dougie Jones reaches an electrifying discovery.
Dougie's loved ones care for him in the hospital, and Mr. C heads towards the coordinates. Meanwhile, Diane makes a confession to the FBI.
Cooper arrives in Twin Peaks.
Cooper and Diane drive 430 miles. Cooper attempts to help a troubled woman he believes to be Laura Palmer.