The first episode of the second season of Twin Peaks, "May the Giant Be With You," originally aired on September 10, 1990, and was directed by series creator David Lynch. This episode features turning points for some major characters as well as several occurrences of supernatural visions. The wounded Agent Cooper (Kyle MacLachlan) has his first visions of the Giant (Carel Struycken), who gives him three clues and takes his ring. At One-Eyed Jacks, the disguised Audrey (Sherilyn Fenn) manages to avoid her father as a client and gets imprisoned by Blackie (Victoria Catlin). Now that Jacques is dead, Leland's (Ray Wise) hair has turned white and his previous grieving has turned to insane happiness, in which he dances and sings "Mairzy Dotes." Donna (Lara Flynn Boyle) also goes through some changes by wearing Laura's sunglasses, smoking cigarettes, and volunteering for the Meals on Wheels program. Maddy (Sheryl Lee) has a brutal vision, and Major Briggs (Don Davis) has his own vivid dream, which he shares with his son, Bobby. At the Sheriff's office, Albert Rosenfeld (Miguel Ferrer) returns and forms a theory with Agent Cooper about the night of Laura's death, which includes the presence of the killer, BOB. After the mill fire, Josie and Catherine are missing, and Shelly and Pete are in the hospital. As Leo (Eric Da Re) barely survives in a coma, the last known living person at the murder scene -- Ronette Pulaski (Phoebe Augustine) -- starts to awaken from her coma to have disturbing visions.

Episode nine of Twin Peaks, "Coma," originally aired on October 6, 1990, and was directed by series creator David Lynch. This episode contains the first of many significant references to owls throughout the series. Agent Cooper learns his old partner, Windom Earle, has escaped a mental institution and is missing. Taking over Laura's old job with Meals on Wheels, Donna delivers food to Mrs. Tremond (Frances Bay) and the magical boy (played by the director's son, Austin Jack Lynch), who delivers the message: "J'ai une âme solitaire," meaning "I have a lonely soul." When the deal with the Icelandic investors gets thwarted by a crazed Leland, Ben and Jerry threaten a scheme to get rid of him. Meanwhile, Bobby and Shelly begin a scheme of their own to deal with the still-comatose Leo. After the Log Lady tells Major Briggs to deliver the message, he meets with Agent Cooper and shows him the message: "The owls are not what they seem." After learning details about Laura's connection to One-Eyed Jacks, Audrey is caught by Blackie. She calls Agent Cooper for help, who is having a dream in which the Giant gives him another clue.

Episode ten of Twin Peaks, "The Man Behind Glass," originally aired on October 13, 1990, and was directed by Lesli Linka Glatter. Agent Cooper tells Albert and Truman about the giant from his dreams, and he finds a letter "B" under Ronette Pulaski's fingernail. He then charts a diagram for the letters he has found so far (R, B, and T). Secretary Lucy Moran (Kimmy Robertson) meets department store clerk Dick Tremayne (Ian Buchanan) for lunch at the Double R diner as she continues to question whether the father of her baby is Dick or the possibly sterile Andy. The One-Armed Man (Al Strobel) comes by the Sheriff's office to sell shoes, but he goes into spasms after seeing the sketch of BOB, leading Cooper to remember one of the giant's messages. At One-Eyed Jacks, Blackie (Victoria Catlin), Nancy (Galyn Gorg), and Jean Renault (Michael Parks) hold Audrey hostage and shoot her with drugs in a scheme to get revenge on Cooper. Meanwhile, James and Maddy are growing closer, and Donna gets angry after seeing them together. At the hospital, a hypnotized Dr. Jacoby reveals that he saw Leland kill Jacques Renault, resulting in Cooper arriving at the Palmer household to arrest Leland. That night, Donna goes to Harold Smith's (Lenny Von Dohlen) house and finds Laura's secret diary.

Episode 11 of Twin Peaks, "Laura's Secret Diary," originally aired on October 20, 1990, and was directed by Todd Holland. At the Sheriff's office, Cooper and Truman interrogate Leland about the murder of Jacques Renault. Andy takes another sterility test to find out if he is capable of being the father of Lucy's baby, while Dick Tremayne offers money for an abortion. At the Double R diner, Donna enlists Maddy's help in a plan to get Laura's diary away from Harold. Meanwhile, Emory Battis (Don Amendolia) is killed and Jean Renault (Michael Parks) shows Ben a video of Audrey, who is still held hostage and drugged at One-Eyed Jacks. When Cooper is required to deliver the ransom money to save Audrey, he asks Truman for the help of the Bookhouse boys. Many characters enter the town of Twin Peaks in this episode: Judge Clinton Sternwood (Royal Dano) arrives at the station; Josie Packard returns with her so-called cousin, Jonathan (Mak Takano); and the elusive Mr. Tojamura (credited as Fumio Yanoguchi) checks into the Great Northern Hotel.

Episode 12 of Twin Peaks, "The Orchid's Curse," originally aired on October 27, 1990, and was directed by Graeme Clifford. This episode features guest star David L. Lander (Squiggy from Laverne & Shirley) as Mr. Pinkel, a salesman who demonstrates equipment to Bobby and Shelly to care for the invalid Leo, who is deemed unable to stand trial. The pregnant Lucy leaves town for a few days, while Deputy Andy Brennan learns that he has a healthy sperm count. Leland Palmer has his trial and is released on bail after Sheriff Truman testifies in his favor. Judge Sternwood (Royal Dano) tells Cooper: "Keep your eye on the woods." At the Great Northern Hotel, the mysterious investor Mr. Tojamura wants in on the Ghostwood Estates deal, with an offer of a large sum of money to Ben Horne. That evening, Jean Renault calls Ben and Cooper with instructions on the ransom exchange for Audrey. Cooper and Truman raid One-Eyed Jacks and are followed by Hank Jennings. They save Audrey with the unexpected help of Deputy Hawk, Blackie is killed, and Jean captures Hank. Meanwhile, Donna and Maddy attempt to steal Laura's secret diary from the increasingly unstable Harold Smith.

Episode 13 of Twin Peaks, "Demons," originally aired on November 3, 1990, and was directed by Lesli Linka Glatter. This episode offers important information on the nature of Killer Bob as a spirit who requires a human host. Donna and Maddy fail at their mission to steal Laura's diary when Harold goes mad and threatens them. After James saves them, Maddy begs him to forget about her and get back with Donna. Agent Cooper takes the rescued Audrey to the Bookhouse. After finding out it was Jean Renault who trying to kill him at One-Eyed Jacks, Cooper returns the ransom money to Ben, who pleads ignorant of the whole scheme. Cooper's supervisor, Chief Gordon Cole (played by series creator David Lynch), arrives in Twin Peaks with a lab report and a message from Windom Earle in the form of a chess move. Josie makes a deal with Ben, gets her money, and is forced to leave town with Jonathan. At the Great Northern Hotel, Mr. Tojomura and Ben have a confrontation, but are interrupted by the crazed Leland's song and dance. The episode ends with the interrogation of the One-Armed Man, who reveals clues about Killer Bob by way of his schizophrenic other self, Mike.

Originally broadcast on November 10, 1990, Episode 14 of Twin Peaks, "Lonely Souls," was written by Mark Frost and directed by David Lynch. This pivotal episode answers some of the series' long-running questions, as well as providing insight into Laura Palmer's killer. Featuring guest singer Julee Cruise, the brutal ending scenes flash between realities. In the morning, Maddy tells Leland and Sarah that she plans to go back to Missoula, MO. Meanwhile, Deputy Hawk searches the murder scene at Harold Smith's house, finding what is left of Laura's secret diary and a suicide note reading "J'ai une ame solitaire" ("I have a lonely soul"). Trying to solve his money problems, Bobby searches Leo's boots and finds some incriminating evidence. Audrey confronts her father about One-Eyed Jacks, and Ben reveals his connection to Laura. After looking over the diary, Cooper has Ben dragged out of his office and placed in a holding cell. At the Blue Pine Lodge, Pete Martell (Jack Nance) discovers the hidden identity of the mysterious Mr. Tojamura. That evening at the Palmers' house, Maddy smells burning oil, Sarah sees a vision of the white horse, and BOB reveals himself. At the Roadhouse, the Log Lady knows what is going on and Cooper sees a vision of the Giant, who warns, "It is happening again."

Episode 15 of Twin Peaks, "Drive With a Dead Girl," originally aired on November 17, 1990, and was directed by Caleb Deschanel. When incompetent lawyer Jerry Horne arrives to represent his brother, Ben, they share a dream sequence from their past of Louise Dombrowski (Emily Fincher) dancing with a flashlight. Lucy arrives back at the Sheriff's office with her sister, Gwen (Kathleen Wilhoite), and the now-fertile Andy faints after seeing Lucy holding a baby. At the Double R Diner, Norma's mother, Vivian (Jane Greer), arrives with her new husband, Ernie (James Booth), who has a secret connection to Hank. Pete Martell visits Ben's jail cell with a tape-recorded proposition from the formerly disguised Catherine that may get him released if he cooperates. Meanwhile, Bobby listens to the tape he found in Leo's boots and plans his own proposition for Ben. Cooper and Truman encounter the unstable Leland, who drives recklessly, sings "Surrey With the Fringe on Top," and dances with his golf club. Cooper has the One-Armed Man examine Ben, leading Cooper to believe that Ben is not the killer. Truman charges Ben with the murder of Laura Palmer, and, for the first time, questions Cooper's investigation tactics. That evening, the body of Madeline Ferguson is found by the water, wrapped in plastic.

Episode 16 of Twin Peaks, "Arbitrary Law," originally aired on December 1, 1990, and was directed by Tim Hunter. This episode features the elusive elements of Cooper's dream from Episode Two finally coming together to crack the case. The evidence shows that Maddy's killer was the same as Laura's, and Albert Rosenfeld and Deputy Hawk show faith in Cooper's declaration that he needs 24 hours to solve the investigation. Meanwhile, the secret identity of Mr. Tojamura is revealed to Ben, only after he signs over the mill and Ghostwood estates. Seeking the connection between the magical boy and Harold Smith's suicide note, Donna visits Mrs. Tremond's house with Agent Cooper and Andy. She receives an envelope with a page from Laura's secret diary that reveals Laura and Cooper had the same dream. Cooper then stages a confrontation at the Roadhouse with suspect Ben and the help of Ed and Hawk. Truman brings Leland, Bobby brings Leo, and Major Briggs arrives unexpectedly with the old waiter. As his visions become clearer, Cooper remembers Laura's message from his dream and the Giant gives him back his ring. The final chaotic conclusion at the Sheriff's office officially answers the question of who killed Laura Palmer.