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 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. 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 that 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 the help of John Justice Wheeler.
Harry sinks into a deep depression after Josie's death. Josie's body holds more questions than 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 'n' 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 sights 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.
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 and Audrey stages an act of civil disobedience.