The town's dark side and secrets become more prominent in Agent Cooper's investigation into who killed Laura Palmer. As the unbelievable details reveal themselves, he risks everything to learn the truth, including his own soul.
A wounded Agent Cooper has a vision of a giant who gives him several clues about the murder of Laura Palmer. Shelly and Pete recover from the mill fire, but Josie and Catherine are missing. Ben and Jerry Horne are not pleased with how the mill fire plan unfolded. Leland Palmer's attitude changes with his hair color. Albert returns to assist the wounded Cooper. Donna gets a mysterious message about Meals on Wheels. Dr. Jacoby recovers from his heart attack, but cannot remember who killed Jacques. Major Briggs has a vision of good things for Bobby. Nadine is in a coma. Leo is a vegetable. Ronnette awakes from her coma after a horrific dream about Bob.
Albert determines that neither Leo nor Jaqcues killed Laura, but he is unable find any leads into who shot Cooper. Cooper says they must find the third man, who he believes to be Bob, the grey haird man. Albert reports that Cooper's ex-partner, Windom Earle, escaped from an insane asylum. Ben Horne can't decide which of the mill ledgers to destroy. The Log Lady tells Major Briggs to deliver a message to Agent Cooper. An Asian man spies on Cooper. Shelly visits Leo in the hospital. Maddy and James discuss a change in Donna's attitude. Leland has a revelation. Bobby tries to convince Shelly to cash in on Leo's insurance money. Audrey is trapped at One Eyed Jack's.
Ronette is attacked in her hospital bed by an unseen person. Jean Reanult, brother of Jaqcues and Bernard, plans to blackmail Ben Horne for the release of Audrey. Donna meets with Harold Smith, a shut-in who had befriended Laura. Albert and Truman have a strange confrontation. Lucy reveals that there's been another man in her life, Dick Treymane (Horne's Department Store, Men's Fashions). Shelly decides not to testify against Leo. Leland offers a clue in the search for Killer Bob. The One-Armed Man leaves Cooper the giant's final clue. Nadine wakes from her coma a changed woman. Jacoby leads Cooper and Truman to Jacques's killer. Donna discovers the secret diary of Laura Palmer.
Leland confesses to killing Jacques Reanult. Andy wants to take a new sperm count test. Rumor spreads that a food critic is coming to Twin Peaks. Jean asks Ben to set a trap for Cooper in exchange for Audrey's life. Cooper agrees to Ben's requests, unaware of the trap. Harold Smith reads from the diary to Donna. Josie returns to Twin Peaks. Cooper asks for help from the Bookhouse Boys, and Harry comes through. Donna and Maddy plot to steal the diary. Judge Sternwood arrives for the trials of Leo and Leland. Dick Tremayne makes a shocking offer to Lucy. The Asian man comes after Josie and Hank.
Cooper discovers he had forgotten about the message under his bed. Shelly and Bobby begin Leo's homecare. Sternwood hears pre-trial motions and declares Leo not fit for trail. Nadine comes home, still thinking she's in high school. A mysterious man, Mr. Tojamura, arrives and offers Ben a sizeable fee for Ghostwood. Cooper agrees to drop Audrey's ransom, but deduces that she's being held at Jack's. Andy's test results are an improvement. Cooper and Truman raid One Eyed Jack's and rescue Audrey, witness several murders, and are saved by Hawk in the process. Jean Renault captures Hank. Harold Smith catches Donna and Maddy trying to steal the diary.
James saves the girls from a tormented Harold. Cooper brings Audrey home. Bobby and Shelly learn that their insurance plans have backfired. Donna tries to convince Truman that Harold Smith has Laura's secret diary. Cooper's boss, Gordon Cole, arrives with an upsetting message for Cooper. Hawk finds the One-Armed Man, who reveals himself as the spirit, Mike. Maddy decides to go home. Jonathan says he's taking Josie back to China. Ben calls Leland back into work. The One Armed Man vows to stop BOB, pointing Cooper towards the Great Northern Hotel.
Cooper and the One-Armed Man inspect guests at the Great Northern. Hawk finds Harold Smith dead by his own hand…with a mysterious suicide note and the diary torn to shreds. Leo speaks to Bobby about "new shoes." Audrey confronts her father about One Eyed Jacks. Shelly tells Norma she has to quit working at the Double R. Norma sees the changed Nadine for the first time. Bobby finds evidence to blackmail Ben Horne for a sizable sum. Audrey goes to Cooper about her father, leading Truman and Cooper to arrest Ben. Tojamora reveals his true identity to Pete. The Log Lady brings Cooper to the Roadhouse, where the Giant appears. Late in the evening, Laura's killer strikes again...
Donna and James wonder why Maddy left so suddenly. Norma's mother arrives with news…she's married a new man, Ernie Niles. Cooper tells Leland they arrested Ben Horne for Laura's murder. Ben tells Jerry the only person who can prove his innocence is the missing Catherine. The One-Armed Man escapes custody. Pete and Truman worry about Josie. Pete tells Ben that Catherine is still alive, and wants to make a deal. Cooper comes face to face with the killer without realizing it. Lucy tells Andy that Dick may be the father. Hank and Ernie know each other from prison. Truman insists on prosecuting Ben Horne. Maddy is found wrapped in plastic.
Albert returns to examine Maddy. Cooper asks for twenty-four hours to finish his case. James and Donna reaffirm their love. Andy accidentally leads Donna and Cooper back to Mrs. Treamond's house. Cooper is given a missing page from Laura's diary, describing the same dream he had. The One Armed man is ill, tells Cooper he has all the clues he needs. Catherine reveals herself to Ben, and he signs the mill back over to her. Leland and Donna learn of Maddy's death. Cooper calls together everyone for a final confrontation. James leaves town. Cooper tricks the killer into revealing himself after decoding the various clues from his dream. The spirit of BOB flees from the killer's body, who dies in Cooper's arms and is welcomed into the next life by Laura. Truman, Cooper, Albert and Major Briggs ponder the existence of Bob, and where he has gone to…
Leland is laid to rest and Sarah Palmer tries to accept all that has happened to her family. Dr. Jacoby returns from Hawaii. Cooper prepares to leave Twin Peaks. Mayor Milford objects to his brothers engagement to a younger woman. Hank and Ernie meet with Jean Renault. Jacoby has Ed enroll Nadine in High School. Audrey and Cooper say goodbye, and Cooper tells her about the death of a woman he loved. Bobby plans to take advantage of Ben's ruin. Cooper is made a Bookhouse Boy. Agent Rodger Hardy arrives to suspend Cooper for his illegal entrance into Canada and his involvement in the murders at One Eyed Jacks. Norma's mother reveals herself to be the critic who wrote a scathing review of the Double R. Josie returns to Truman. Major Briggs vanishes in a bright light while fishing with Cooper.
Mrs. Briggs talks about her husband's disappearance into the woods. Nadine is put on the wrestling team, where she falls for Mike Nelson. James is hired by a mysterious wealthy woman named Evelyn Marsh. Dick takes on an orphan named Little Nicky. The case against Cooper will be handled by DEA Agent Denis (Denise) Bryson. Hank tells Ben that Jean Renault has taken over One Eyed Jacks. Windom Earle contacts Cooper with an omnious message. Dougie Milford weds Lanna Budding. Josie asks Catherine for protection. Andrew Packard comes out of hiding, very much alive.
Ben takes Bobby under his wing in a hope to destroy Hank and Jean. However, Ben's mental state is starting to crack. Cooper starts to look at buying real estate. Major Briggs's supervisor reveals that Briggs was studying transmissions from the woods. Andy and Dick learn of Little Nicky's troubled life. James meets Malcom, the chauffer for the Marsh family. Dougie Milford dies on his honeymoon, and the major blames Lana. Cooper finds drugs at Dead Dog Farms. Dick thinks Nicky is trying to kill him. Evelyn starts an affair with James. Ben begins to reenact the civil war. Audrey produces photos that may save Cooper. Hank catches Ed and Norma in an embrace. Denise and Cooper enlist Ernie Niles to ensnare Jean Renault. Major Briggs returns as mysteriously as he had vanished.
Major Briggs has no memory of the place he was taken, but now has an odd tattoo on his neck. Andy and Dick break into Little Nicky's files. Mike and Nadine begin an affair. Shelly and Bobby's love is strained. Evelyn asks James to kill her husband. Hank attacks Big Ed, but is beaten by Nadine. Ben slips deeper into his fantasy life. When the drug bust goes bad, Cooper is taken hostage by Jean Renault. Leo Johnson comes back to life. After physical and mental torture by Renault, Cooper is saved by a quick thinking Bryson and Truman.
Later that night, an explosion and blackout empties out the police station, and when Cooper and Truman return, they find a gruesome scene let by Windom Earle.
Windom Earle has taken his first victim in the deadly chess game. Audrey tells Bobby they have to save Ben from his Civil War fantasy. Leo awakes and attacks Shelly, but Bobby is able to fend him off. Doc Hayward offers the true story of Little Nicky's past. Cooper reveals his rivalry with Earle: they were partners when Cooper fell in love with Caroline, Earle's wife. Earle went mad, killing Caroline and wounding Cooper. Mr. Marsh is killed. Donna confronts Evelyn. After a heated confrontation Mayor Milford and Lana end up lovers. Andrew Pakcard reveals himself to Pete, and tells him Josie has been working for his old enemy Thomas Eckheardt. Cooper suspects Josie in the murder of Jonathan. Eckheardt arrives in Twin Peaks, and Leo Johnson finds himself in the company of Windom Earle.
The police look for James in the Marsh murder. Bobby and Shelly tell Truman Leo escaped and Bobby reveals that he saw Hank shoot Leo the night the mill burned. Albert returns to Twin Peaks with information on Windom Earle, and ends up looking at Josie for the murder of Jonathan and the attempted murder of Cooper. Nadine ‘breaks up' with Ed. Dr. Jacoby, Audrey, Bobby and Jerry try to end Ben's fantasy life. Donna and James escape from the Marsh home. Pete offers to help Cooper force a stalemate with Earle. Earle holds Leo as a slave. Shelly comes back to work. Eckheardt tells Catherine he wants Josie back. Earle leaves a 'present' and another omnious message for Cooper.
Truman puts Hank in prison for the attempted murder of Leo, while Hank points the finger at Josie for the murder of Andrew Packard. Albert reveals that Josie shot Cooper. Ben enlists John Justice Wheeler to help him stop the Ghostwood plans. Earle sends a poem to Donna, Shelly and Audrey. Ben decides to "save the pine weasel." Norma learns her sister Annie is coming to town. Ed proposes to Norma. James leaves Twin Peaks.
Caught in her own web of deceit, Josie murders Eckheardt, but is caught by Cooper and Truman. She confesses to shooting Cooper, but before they can act, Josie dies in Harry's arms. As she passes away, Cooper has a vision of BOB and the Little Man. Josie's soul is trapped in a door pull.
Harry sinks into a deep depression after Josie's death. Josie's body holds more questions then answers. Norma's troubled sister, Annie, arrives in Twin Peaks. Wheeler and Audrey hit it off. Cooper's stalemate angers Earle. Eckheardt's assistant, Jones, leaves a puzzle for Catherine. Windom Earle visits Donna. The Log Lady and Major Briggs share similar tattoos and go to Cooper with them. The Miss Twin Peaks contest is coming up, and Norma wants Shelly to enter. Cooper meets and is taken with Annie. Ben holds a Save the Pine Weasel fashion show that goes wrong. Jones slips into Harry's bed.
Harry is attacked by Jones in his sleep. Audrey and Wheeler begin a relationship. Gordon Cole returns with a report that Windom Earle worked with Major Briggs on Project Bluebook. Cole reinstates Cooper in the FBI. Earle plans to kill the winner of Miss Twin Peaks. Donna spies Eileen Hayward paying a mysterious visit to Ben Horne. Gordon Cole believes Shelly can cure his hearing loss. Annie recognizes the two tattoos are coming from Owl Cave. Earle visits Audrey. Cooper, Truman, Hawk and Andy visit Owl Cave. Cooper learns Annie has had a difficult life and offers to help her. Earle uncovers a petroglyph in Owl Cave.
Cooper and company find the mysterious petroglyph. Windom Earle befriends a rock and roll youth, and tells him tales of places called the White and Black Lodge. Pete helps Catherine open the first puzzle box. Lana wants Milford to rig Miss Twin Peaks. Annie and Cooper go for a nature walk. Cooper finds the poem Earle sent to the girls. He tells Harry it's a poem he once gave to Caroline. Major Briggs agrees to look into Earle's Project Bluebook work. Cooper deduces Leo Johnson is working with Earle. Shelly, Lucy, Donna, Nadine, Lana and Audrey enter Miss Twin Peaks. Mike tells Bobby about Nadine's special bedroom talents. Cole says goodbye to Shelly. Donna wants to know what is going on between her mom and Ben Horne. Treymayne hosts a wine tasting party. Windom Earle leaves his next victim and a terrifying promise for Cooper: "Next time, it will be someone you know."
Bobby and Shelly reaffirm their love. Cooper calls Shelly, Donna and Audrey together to warn them about Earle. Briggs shows Cooper a tape of Windom Earle making a report on his quest for the Black Lodge. Donna discovers pictures of her mom and Ben Horne. Wheeler is called away on an emergency. Leo worries about Shelly. Doc Hayward tells Ben to stay away from Eileen. Townsfolk have strange tremors in their hands. Pete has a vision of Josie. Windom Earle takes Major Briggs captive. Andrew and Catherine open the next box, only to find another one inside. A drugged Briggs tells Earle how to open the lodge doorway. Big Ed is able to break up with Nadine and ask Norma to marry him. Audrey and Pete chase after Wheeler…Audrey and Wheeler make love before he leaves. Cooper takes Annie dancing, and convinces her to run for Miss Twin Peaks. The Giant visits Cooper with a warning. Windom Earle discovers the cave painting is a map. BOB reappears.
Windom Earle sets his sites on the Miss Twin Peaks contest. Lucy chooses a father for her baby. Leo is punished when he frees Major Briggs. Cooper unlocks the key to entering the Black Lodge. Annie and Dale make a commitment to each other. Catherine and Andrew find a mysterious key. Donna confronts Ben Horne. The Miss Twin Peaks contest ends in chaos. Windom Earle kidnaps Annie. Andy deciphers the Owl Cave puzzle.
Agent Cooper follows Windom Earle and Annie into the depths of the Black Lodge. Big Ed and Norma get a shock when Nadine suffers head trauma. Andrew and Pete unlock Eckheart's final box while Audrey stages her act of civil disobedience. Dr. Hayward and Ben Horne have a final confrontation. Shelly and Bobby plan their future. Dr. Jacoby and Mrs. Palmer have a message for Major Briggs. Cooper faces his destiny in the Black Lodge.