Bob then turns on Cooper, who experiences fear for the first time in the Lodge. Laura was also addicted to cocaine, which she obtained by coercing Bobby into doing business with Jacques. He begs for forgiveness, sees a vision of Laura welcoming him into the afterlife, and dies in Cooper's arms. She and Maddy attempt to steal it from him, but Harold catches them in the act, loses all faith in humanity, and hangs himself in his orchid greenhouse. Some time after entering the Lodge, Cooper and Annie reappear in the woods. When Annie wins the Miss Twin Peaks contest, Earle kidnaps her and takes her to the Black Lodge entrance in Glastonbury Grove.
Cooper learns that Bob, the Giant, and the Man From Another Place all come from one of the two lodges. Cooper interprets these events to mean that Renault is the murderer and, with Truman's help, tracks Renault to One-Eyed Jack's, a brothel owned by Horne across the border in Canada. Mike says that Laura's murderer is a similar entity, Killer Bob, a feral, denim-clad man with long gray hair. Cooper tries to discover the origin and whereabouts of Bob, and learns more about the mysteries of the dark woods surrounding Twin Peaks. In 1989, logger Pete Martell discovers a naked corpse wrapped in plastic on the bank of a river outside the town of Twin Peaks, Washington. Cooper agrees and Earle stabs him.
The authorities discover that Laura has been living a double life. The officers take possession of Laura's secret diary, and learn that Bob, a friend of her father's, raped her repeatedly as a child and that she began using drugs to cope. Searching for Annie and Earle, Cooper encounters doppelgängers of various dead people, including Maddy Ferguson and Leland Palmer, who taunt him with strange denials, warnings, and falsehoods. Cooper finds himself decades older with Laura and a dwarf in a red business suit, who engages in coded dialogue with Cooper. Donna takes on Laura's old route for the Meals on Wheels program in the hopes of finding more clues to Laura's murder.
Cooper and the sheriff's department find the one-armed man from Cooper's dream, a traveling shoe salesman named Phillip Gerard. Lawrence Jacoby, was obsessed with Laura, but he is proven innocent of the murder. Meanwhile, Bob restlessly seeks another host. The next morning, Cooper tells Truman that, if he can decipher the dream, he will know who killed Laura. He was committed to a mental institution but escaped, hiding out in the woods near Twin Peaks. Cooper flees, pursued by Bob and a doppelgänger of himself.
Cooper has a dream in which he is approached by a one-armed otherworldly being who calls himself Mike. Cooper returns to his room following Jacques's arrest and is shot by a masked gunman. Gerard knows a Bob, the veterinarian who treats Renault's pet bird. A badly injured second girl, Ronette Pulaski, is discovered in a fugue state. Cooper doubts Horne's guilt, so he gathers all of his suspects in the belief that he will receive a sign to help him identify the killer. With clues from Deputy Andy and the Log Lady, Cooper discovers the entrance to the Lodge, which turns out to be the red-curtained room from his dream. Seconds later, Killer Bob appears and reverses time in the Lodge.
He is greeted by the Man From Another Place, the giant, and the spirit of Laura Palmer, who each give Cooper coded prophecies about his future and demonstrate the properties of the Black Lodge, which defies the laws of time and space. The same night, Horne orders Leo to burn down the lumber mill with Catherine trapped inside and has Leo gunned down by Hank Jennings to ensure Leo's silence. Annie is bloodied and hospitalized, but Cooper's injuries are minor enough that Doctor Hayward is able to treat them in Cooper's room at the Great Northern Hotel. Josie Packard dies mysteriously during Truman and Cooper's attempt to apprehend her for shooting Cooper. He plays a twisted game of chess with Cooper in which someone dies each time he captures an opponent's piece. At the moment of her death, Bob briefly appears to Cooper, drawn by her fear. Horne's sultry, troubled daughter, Audrey, becomes infatuated with Cooper and spies for clues in an effort to gain his affections.
Bob tells Cooper that Earle cannot ask for his soul and then kills Earle and takes his soul. Upon waking, Cooper asks about Annie's condition, and then states he needs to brush his teeth. Earle went mad, killed Caroline, and stabbed Cooper. With the help of Laura's cousin Maddy Ferguson, Donna and James discover that Laura's psychiatrist, Dr. The lawmen question whether Leland was truly possessed or mentally ill, and considers the possibility that Bob might still stalk the community of Twin Peaks in search of a new host.
He then rams his head into the mirror and, while laughing maniacally, repeatedly mocks his earlier question about Annie's condition. . Cooper believes that the killer is Ben Horne, but Leland is revealed to be Bob when he brutally kills Maddy. They are discovered by Sheriff Truman, who has been waiting for them since he saw Cooper disappear. Leland, learning that Renault has been arrested, sneaks into the hospital and murders him.
Cooper realizes that Earle's real reason for being in Twin Peaks is to gain entrance into the Black Lodge and harness its power for himself, and that his chess game has been an elaborate decoy. The Giant appears and confirms that Leland is Bob's host and Laura's and Maddy's killer. The doppelgängers eventually lead Cooper to Earle, who demands that Cooper give up his soul in exchange for Annie's life. Cooper falls in love with a new girl in town, Annie Blackburn. Cooper informs the community that Laura's death matches the signature of a killer who murdered another girl in southwestern Washington the previous year, and that evidence indicates the killer lives in Twin Peaks.