Cooper’s body is occupied by Bob; since Cooper is still in the Black Lodge, Bob cannot even pretend to be him. His friends assume he was driven insane and regretfully consign him to an asylum in Portland, where he amuses himself tormenting the other inmates and saying cruel things to Cooper’s friends when they visit.
Cooper, meanwhile, is bent on exploring the Black Lodge, and he gathers together Laura, Maddy, and Agent Desmond to solve the riddles of the place.
Annie visits the asylum and figures out immediately that Cooper isn’t in there. She spends the rest of the season discovering a way to get Coop back into his body, and expel Bob. It means building her courage and taking risks, so there’s some nice char growth. She also learns that Miss Twin Peaks isn’t just a superficial title; it makes her a member of the Bookhouse Boys (So Norma is as well) and makes her privy to secret information. Like, she’s given access to hidden rooms at the public library, that kind of thing.
Audrey and Pete both wake up in the hospital, virtually unscathed, though Andrew is blown to bits. Discussing this weird phenomenon, it turns out they both had a vision of the walls curling suddenly in to shield them…and the walls had Josie’s face. It will eventually become clear that Josie has become a sort of Dryad that can move through infrastructure all over town, and she becomes instrumental in finding the White Lodge, and will end up as one of the guardians who dwell there.
Harry becomes obsessed with the lore of the Lodges and spends much of his time uncovering vital clues.
Lucy and Andy have their baby. They’re not terribly important for this story arc, but they’re around. Hawk as well. They’re the beacons of normality.
Sarah Palmer decides to go on a long trip to the southwest to clear her head and mourn her dead. She ends up lost in a desert, begins to have cryptic visions, and is rescued by THE white horse, which takes her to a medicine man who gives her vital information needed back in Twin Peaks. Her car is wrecked, so she decides to hitchhike north. By a startling coincidence, she’s picked up by James, who has been having dreams about Donna and is worried.
Early in the season, it will be revealed that Bob is not unique; that there are many spirits who feed on pain, and he has prepared a way for them by making doors at every place he left a pile with a piece of jewelry. The doors will all open at a specific time. Perhaps this is the info given to Sarah; however they learn it, it ups the stakes. There’s a ticking clock, so to speak. The White Lodge needs to be found and the Keeper awoken, or bad bad things will happen.
When Ben wakes up, Donna is sitting with him. She has a succinct little speech about being devoted to the truth, because lies killed her friends; but that she knows in her gut that Ben is not her father, because he is happy to live a lie, and maybe he should go back to the sleazy persona he does so well. He has, after all, utterly failed to be a “good person.” When he groggily objects, saying it felt good to try and be good, and that he feels guilty because he was part of the sickness of the world. He confesses to owning the brothel and making shady business deals and all the rest. She smiles that little smile of hers and tells him to keep doing good, by all means. But stop trying to ease his guilt, because that’s just causing more damage. Just live with it, she tells him. Get over yourself. Save the stupid pine weasel and leave your past alone. She puts a cigar on the bedside table and leaves. He picks it up and lights it thoughtfully.
Leo falls asleep and his jaw relaxes. He’s jerked awake in terror by the cage hitting his head, but the damn thing doesn’t break. He lays there for a while looking at the intact cage full of spiders, and starts crying. When Major Briggs eventually remembers where he was held and leads a party to the cabin to rescue him, he has vanished. Leo’s ultimate fate can remain a mystery.
Major Briggs decides to write his memoirs. He writes like he speaks, but no one has the heart to tell him it’s unreadably dense. Someone accuses him of plagiarizing obscure 18th century fiction. When Lucy reads it, though, she loves it; and she points out a vital clue hidden with in the text that point to the White Lodge.
Bobby graduates and goes to business school. Shelly is super supportive, but she’s sick of living in Leo’s half-finished house. She either sells the property, or finds a helpful contractor to finish the walls and redecorate. Or maybe she just burns it down. I dunno. But that house has to undergo some changes, so Shelly can get some freedom from her past.
Nadine demands that Dr. Jacoby stop fiddling around with wimpy treatments and “do something that works.” He decides to try a hypnotism method he’s only ever heard about, and we get a good chunk of time devoted to her inner journey, recalling her life (and death) with Ed, her time with Mike, and a bunch of stuff from her childhood. A strange experience in the woods at the age of six which gave her super strength might be a nice detail; it could be Lodge related, too. Her drapes fixation might even have an explanation. When she comes out of it, she will gently tell Ed that it’s not his fault, but the happiest she’s ever been was when she wasn’t his wife, and she might even go to Mike and ask if he wants an older woman who doesn’t happen to have amnesia. Which, of course he does. Could be a very touching scene.
Ed gets Norma. They decide to take a honeymoon. Norma leaves Shelly in charge of the diner, and James arrives just in time to get handed the gas station. He isn’t elated, but he doesn’t argue. He knows what this means to his uncle.
Donna and James have a tentative reunion; neither is sure how the other is feeling. But something funny will happen, and they both laugh, and that lightens the mood. James gives Donna his travel journal, and Donna fills James in on the Cooper situation. They go to Portland to see him, and he makes it clear that he is Bob, not Dale; and that he killed Laura and Maddy. He taunts them with it. James threatens to kill him, but he laughs and says that in that case, they’d lose Cooper, but Bob would be around forever. They leave perplexed.
Katherine is dismayed at Andrew’s real death, and she resents Pete for surviving. She starts to see Josie in the paneling and the furniture, and wonders if she’s going insane. Ben tells her that the weasel might be a red herring, but that Ghostwood Estates is a mistake for much more supernatural reasons; he had planned it knowing it would either save the town from evil or drown the town in evil, and he was willing to take that risk once, but no longer. She goes into the woods by herself to see what the fuss is about, and has a really weird and trippy time. Maybe she gets a vision of Andrew, giving her a warning, or maybe Josie comes out to mess with her. Whatever happens, she gets pretty spooked.
The story will culminate in Bob escaping the nuthouse, the portals opening, Cooper and the gang tricking the Black Lodge into releasing them, Mike growing spirit wings, Annie arriving with the White Lodge posse, glowing leylines, alarums and excursions, and a battle of competing realities which is won, at the last possible second, by Laura’s spirit, which steps forward and annihilates Bob, maybe even forever.
When the smoke clears, our heroes have won, but they don’t know for how long. Everyone goes back to normal life. Or as normal as it gets around here.
The endcap scene is Billy Zane (John, yes, I know, but he’s just so Billy Zane) coming back and saying something about how this sleepy little town hasn’t changed at all. Audrey smiles knowingly.