Albert determines that neither Leo nor Jacques 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 gray-haired man.
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Ronette is attacked in her hospital bed by an unseen person. Jean Renault, brother of Jacques and Bernard, plans to blackmail Ben Horne for the release of Audrey. Donna meets with Harold Smith, a shut-in who had befriended Laura.
Leland confesses to killing Jacques Renault. 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 discovers he had forgotten about the message under his bed. Shelly and Bobby begin Leo's home care. Sternwood hears pretrial motions and declares Leo not fit for trial. Nadine comes home, still thinking she's in high school.
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 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."
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.
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. Tremond's house.
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.
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.
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.
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.
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.
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.
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.
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..
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.
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.
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.
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.
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 Eckhardt's final box while Audrey stages her act of civil disobedience.