Season 2
Lying hurt in his hotel room, Cooper has a vision in which a giant appears and reveals three clues: "There is a man in a smiling bag," "the owls are not what they seem," and "without chemicals, he points." He takes a gold ring off Cooper's finger and explains that when Cooper understands the three premonitions, his ring will be returned. Leo Johnson survives his shooting but is left brain-damaged. Catherine Martell disappears, presumed killed in the mill fire. Leland Palmer, whose hair has turned white overnight, returns to work but behaves erratically. Cooper deduces that the "man in the smiling bag" is the corpse of Jacques Renault in a body bag.
MIKE is inhabiting the body of Phillip Gerard. His personality surfaces when Gerard forgoes the use of a certain drug. MIKE reveals that he and BOB once collaborated in killing humans and that BOB is similarly inhabiting a man in the town. Cooper and the sheriff's department use MIKE, in control of Gerard's body, to help find BOB ("without chemicals, he points"). Donna befriends an agoraphobic orchid grower named Harold Smith whom Laura entrusted with her second, secret diary. Harold catches Donna and Maddy attempting to steal the diary from him and hangs himself in despair. Cooper and the sheriff's department take possession of Laura's secret diary, and learn that BOB, a friend of her father's, had been sexually abusing her since childhood and she used drugs to cope. They initially suspect that the killer is Ben Horne and arrest him, but Leland Palmer is revealed to viewers to be BOB's host when he kills Maddy.
Cooper begins to doubt 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. The Giant appears and confirms that Leland is BOB's host and Laura's and Maddy's killer, giving Cooper back his ring. Cooper and Truman take Leland into custody. In control of Leland's body, BOB admits to a string of murders, before forcing Leland to commit suicide. As Leland dies, he is freed of BOB's influence and begs for forgiveness. BOB's spirit disappears into the woods in the form of an owl and the lawmen wonder if he will reappear.Cooper is set to leave Twin Peaks when he is framed for drug trafficking by Jean Renault and is suspended from the FBI. Renault holds Cooper responsible for the death of his brothers, Jacques and Bernard. Jean Renault is killed in a shootout with police, and Cooper is cleared of all charges.
Windom Earle, Cooper's former mentor and FBI partner, escapes from a mental institution and comes to Twin Peaks. Cooper had previously been having an affair with Earle's wife, Caroline, while she was under his protection as a witness to a federal crime. Earle murdered Caroline and wounded Cooper. He now engages Cooper in a twisted game of chess during which Earle murders someone whenever a piece is captured.Investigating BOB's origin and whereabouts with the help of Major Garland Briggs, Cooper learns of the existence of the White Lodge and the Black Lodge, two extra-dimensional realms whose entrances are somewhere in the woods surrounding Twin Peaks. Catherine returns to town disguised as a Japanese businessman, having survived the mill fire, and manipulates Ben Horne into signing the Ghostwood project over to her. Andrew Packard, Josie's husband, is revealed to be still alive while Josie Packard is revealed to be the person who shot Cooper at the end of the first season. Andrew forces Josie to confront his business rival and her tormentor from Hong Kong, the sinister Thomas Eckhardt. Josie kills Eckhardt, but she mysteriously dies when Truman and Cooper try to apprehend her.
Cooper falls in love with a new arrival in town, Annie Blackburn. Earle captures the brain-damaged Leo for use as a henchman and abandons his chess game with Cooper. When Annie wins the Miss Twin Peaks contest, Earle kidnaps her and takes her to the entrance to the Black Lodge, whose power he seeks to use for himself.Through a series of clues Cooper discovers the entrance to the Black Lodge, which turns out to be the strange, red-curtained room from his dream. He is greeted by the Man From Another Place, the Giant, and Laura Palmer, who each give Cooper cryptic messages. Searching for Annie and Earle, Cooper encounters doppelgängers of various people, including Maddy Ferguson and Leland Palmer. Cooper finds Earle, who demands Cooper's soul in exchange for Annie's life. Cooper agrees but BOB appears and takes Earle's soul for himself. BOB then turns to Cooper, who is chased through the lodge by a doppelgänger of himself.
Outside the lodge, Andrew Packard, Pete Martell and Audrey Horne are caught in an explosion at a bank vault, a trap laid by the dead Eckhardt.Cooper and Annie reappear in the woods, both injured. Annie is taken to the hospital but Cooper recovers in his room at the Great Northern Hotel. It becomes clear that the "Cooper" who emerged from the Lodge is in fact his doppelgänger, under BOB's control. He smashes his head into a bathroom mirror and laughs maniacally.
