Cooper recovers from his gunshot wounds, has a vision about Laura's murder and gets some more clues. Shelley and Pete are also recovering from the fire, but find that Josie and Catherine are missing. Ben and Jerry Home are not happy how everything went down with the mill fire and Leland has a new attitude. Albert asks to help Cooper and Donna gets a strange message from Meals on Wheels. After having a heart attack, Dr. Jacoby is recovering, but doesn't remember who killed Jacques. Major Briggs has a vision that good things are coming to Bobby. Nadine falls into a coma and Leo is incoherent. Ronnette wakes up from her coma after having a nightmare about Bob, the man from everyone's dreams.
Albert tells everyone Leo and Jacques are cleared as suspects, but he is still unsure on who shot Cooper. He and Cooper hunt down the third man. Windon Earle, Cooper's former partner, escapes from the insane asylum and Ben Home has problem deciding which ledgers of the mill to destroy. The Log Lady tells Major Biggs to give a message to Cooper. An Asian man spies on Cooper and Shelly visits Leo in the hospital. Bobby attempts to persuade Shelly to collect Leo's insurance money. Audrey finds herself trapped at One Eyed Jack's.
An unseen person attacks Ronette at the hospital. Jacques brother, Jean, and Bernard plan to get Audrey out of One Eyed Jack's by blackmailing Ben Home. Donna meets with a shut-in who was friends with Laura and Albert and Truman have a confrontation that turns strange. Lucy tells everyone she has a new man named Dick Tremayne. Shelly doesn't testify against Leo and Leland gives a clue that helps them get closer to Bob. Cooper gets the giant's final clue and Nadine wakes up from her coma. She is a changed woman and Jacoby leads Cooper and Truman to Jacques's killer. Donna finds a diary Laura kept in secret.
Leland confesses to killing Jacques and Andy demands a sperm count test. A food critic is supposedly coming to the town and Jean asks Ben to set a trap for Cooper to get Audrey out. Unaware it is a trap, Cooper agrees with Ben. Harold Smith reads the diary Donna found and Josie decides to return to Twin Peaks. Cooper asks for some help from the Bookhouse Boys and Harry follows through. Donna and Maddy plan to steal the diary and Judge Sternwood comes for Leland and Leo's trials. Dick Tremayne offers Lucy something that shocks her. Josie and Hank are hunted by the Asian man.
Cooper realizes he forgot about the message he put under his bed and Shelly and Booby tend to Leo at home. Sternwood says Leo is not fit to go to trial. Nadine goes home, but still thinks she is in high school. Mr. Tonjamura comes and offers Ben a fee for Ghostwood. Cooper agrees to give Audrey's ransom, but finds out she is being held at One Eyed Jack's. Andy sees his test results show improvement and Cooper and Truman raid Jack's. They manage to rescue Audrey and are saved by Hawk. Jean catches Hawk. Harold catches Donna and Maddy trying to take the diary.
James comes to Donna and Maddy's rescue and Cooper brings Audrey home. The plans Bobby and Shelly have for the insurance money backfire and Donna tries to tell Truman about the whereabouts of Laura's diary. Gordon Cole, Cooper's boss, comes with bad news for Cooper. The One Armed Man reveals to Hawk that he is possessed by a spirit named Mike. Maddy goes home and Jonathan tells Josie he is going back to China. Ben calls Leland into work and the One Armed Man vows to take down Bob and points Cooper to a hotel, the same hotel where he was shot.
At the hotel, Cooper and the One-Armed Man inspect the guests entering. Hawk finds Harold dead with a suicide note and a torn diary. Leo talks to Bobby and Audrey confronts her father. She talks about One Eyed Jacks. Shelly tells Norma to stop working and Norma sees the changed Nadine for the first time. Booby finds blackmail evidence on Ben and Audrey goes to Cooper with information about her father. Ben is arrested and Tojamora reveals his real name. The Giant appears to Cooper and Laura's killer strikes again.
Jerry attempts to get a lawyer for Ben. Cooper doesn't believe Ben was the killer, but Truman doesn't agree. Pete visits Ben and plays a message from Catherine. She agrees to be his alibi, but he needs to surrender all his property to her. Leland is under the possession of Bob and Maddy is stuffed into a golf bag. Norma's mother, Vivian, comes with her new husband. Lucy and Andy meet up and Andy tells her he wants to get back together. The one-armed man escapes police custody and warns that Bob is close.
Albert examines Maddy's body and Cooper asks for an extension on the case. James and Donna rekindle their love and Andy leads Donna and Cooper to Mrs. Tremond's home. Cooper is handed a piece from Laura's diary which outlines the dream he had. The One-Armed Man gives Cooper more clues and Catherine reveals who she is to Ben. Leland and Donna find Maddy's body and Cooper calls for a confrontation. Cooper manages to get the killer to come forward. The body is released from Bob's spirit, but dies. Everyone wonders what happened to Bob.
Leland is buried and Sarah Palmer has a hard time accepting all the suffering. Dr. Jacoby comes back as Cooper gets ready to leave. Mayor Milford refuses his brother to marry a younger woman and Hank and Ernie meet Jean. Jacoby tells Ed to send Nadine to High School. Audrey and Cooper exchange goodbyes and Cooper opens up to her about a woman he loved. Bobby has plans with Ben's property and Cooper is made Bookhouse Boy. Agent Hardy comes and suspends Cooper for the illegal activity he has been doing. Norma's mom reveals she was the critic who wrote the bad review on the Double R. Josie returns to Truman and Major Briggs disappears while fishing with Cooper.
The disappearance of Mr. Briggs is the talk of the town. Nadine joins the wrestling team and likes Mike Nelson. Evelyn Marsh is hired by James and Dick takes an orphan named 'Little Nicky' in. Cooper's case is to be handled by DEA Agent Denis Bryson. Ben is told that Jean has taken over One Eyed Jack's affairs. Windom contacts Cooper with a strange message and Dougie Milford marries Lanna. Josie asks Catherine to protect her and Andrew Packard comes out of hiding after being thought dead for many years.
In order to destroy Hank and Jean, Ben tells Bobby what he plans to do. It is clear though, that Ben's mental state is cracking. Cooper looks into buying a house and Brigg's supervisor says Briggs was studying transmissions coming from the woods. Andy and Dick find out more about Little Nicky and not all is positive. James meets Malcolm, a chauffeur of the Marsh family. Dougie Milford dies while on a honeymoon and the blame is on Lana. Drugs are found at Dead Dog Farms and Dick tells Andy that Nicki is tying to kill him. Evelyn and James have an affair and Audrey shows photos that could save Cooper. Hank catches Ed and Nora hugging and Denise and Cooper get Ernie Niles to help trap Jean. Briggs returns and it is a mystery to what happened to him.
Major Briggs has no recollection of the night he was taken, but there is a tattoo on his neck. Andy and Dick get into the files of Little Nicky and Mike and Nadine have an affair. Shelly and Bobby have trouble connecting and Evelyn tells James to kill her husband. Hank tries to attack Big Ed, but is stopped by Nadine. Ben starts to fall into his fantasy life more and Cooper is taken hostage when a drug bust goes bad. Leo comes back to life. Cooper is saved by Bryson and Truman after being tortured by Jean.
Cooper talks about Windom Earle to Truman and Leo awakens from his coma. He has changed and Bobby and Audrey decide whether or not to do business together as they try to save Ben. Evelyn's husband is killed and James finds out it was all a set up. Josie's former lover, Thomas Eckhardt, comes back in her life and Windom Earle is revealed.
After finding some evidence to who shot him, Cooper enlists the help of Pete, the chess master of the town. Donna pleads to save James's life, who is the main suspect in the Marsh murder. Shelly goes back to work and Nadine breaks up with Ed. Catherine uses Josie so she can lure Eckhardt away.
Ed proposes to Norma and James and Donna decide to break things off. Audrey is reacquainted with an admirer from her past. Earle mails a puzzle for Audrey, Shelly and Donna to piece together. Hank is arrested for the murder of Leo, but he accuses someone else. Josie meets Eckhardt and things don't go the way she plans.
Annie, Norma's sister comes to Twin Peaks and Cooper takes a liking to her. Truman is depressed and Eckhardt leaves Catherine an intricate puzzle to figure out. The Miss Twin Peaks pageant comes and Ben figures out a way to stop Catherine and save a pine weasel that is endangered in the process.
While sleeping, Harry is attacked. Audrey and Wheeler begin to have a relationship and Gordon Cole comes with a report saying Windom Earle helped work on Project Bluebook. Cole reinstates Cooper to the FBI and Earle plans to kill whoever wins Miss Twin Peaks. Donna sees Eileen visiting Ben and Gordon Cole believes Shelly will be able to cure his hearing loss. Annie recognizes the tattoos are coming from Owl Cave and after hearing of her terrible life, Cooper offers to help Annie. A petroglyph is uncovered in Owl Cave by Earle.
Cooper and the others find the petroglyph and Windom Earle becomes friends with a kid. He tells him about White and Black Lodge. Pete helps Catherine with the puzzle and Lana wants the Miss Twin Peaks pageant to be rigged. Annie and Cooper go on a walk and he finds a poem Earle sent the girls. He tells Harry it is a poem given to Caroline. Major Briggs looks into Earle's Project Bluebook and Cooper realizes Earle and Leo are working together. Shelly, Lucy, Donna, Nadine, Lana and Audrey all enter the contest and Mike tells Bobby what Nadine can do in the bedroom. Cole parts with Shelly and Donna wants to know more about Benand her mom. Treymayne hosts a wine tasting and Windom Earle leaves his next victim with a note that is personal to Cooper.
Major Briggs is captured by Earle and is interrogated about what he knows about Owl Cave. Cooper gets a message from the other side and Donna sees an interesting note on her birth certificate. Wheeler leaves town suddenly without giving Audrey a chance to say goodbye to him.
Part of the secret of the Black Lodge is found out by Andy, Cooper and Truman. Cooper helps Annie set up for Miss Twin Peaks and Major Briggs manages to escape from Earle. Catherine is still trying to figure out the puzzle and Ed breaks up with Nadine because he wants to move forward with Norma and his plans. Terror strikes the Miss Twin Peaks pageant.
Cooper makes his way to Black Lodge by following Annie and Earle. Nadine suffers head trauma and Big Ed and Norma get the shock of their lives. Andrew and Pete manage to unlock the puzzle of the final box and Audrey gets into trouble. Dr. Hayward and Ben have a confrontation and Shelly and Bobby look to their future. Dr. Jacoby and Mrs. Palmer give a message to Major Briggs. Cooper comes face to face with his destiny while in Black Lodge.