As Sam and Dean stop for supper, a hunter named Annie Hawkins calls Dean. She offers her condolences on Bobby’s death and tells Dean that she has some old books of Bobby’s. Since she’s in the neighborhood of Bodega Bay where the Winchesters are, she suggests that they meet her at the Crow’s Nest Inn the next day after she finishes a case so she can hand them over.
Two teenagers, Dudley Scott and Debbie Tellen, are making out in an old house. When Annie pulls up outside, they panic and start to run. However, a hulking figure of a man appears in the hallway ahead of them, tells them that they shouldn’t have come there, and charges at them. A few minutes later, Annie comes in and finds the two teenagers, dead. Her flashlight flickers and the door slams shut behind her.
The next day, Annie never shows to meet Sam and Dean at the restaurant. After reading about Leviathan Dick Roman funding archaeological sites, Dean calls Annie and doesn’t get an answer. Sam asks if he realizes that Annie had a relationship with Bobby, and both brothers realize that they had a thing with her as well at separate times. When Annie doesn’t pick up, Dean pours himself a drink from Bobby’s flask and admits that it’s probably a good thing that Bobby didn’t come back as a ghost as he suspected. After Dean sets the flask down, he fails to notice it moving slightly on its own.
Out at the car, Sam suggests that Dean put the flask away for good because of its association with Bobby, but Dean say that he’s not ready. As they drive to Annie’s hotel room, they’re unaware that Bobby’s spirit is in the back of their car. At the hotel they find Annie’s notes about a local haunted house, the Van Ness House. According to the articles, there were numerous disappearances in the area a few years back, then they stopped but recently started up again. While the brothers go over Annie’s files, Bobby tries to move something, but finds the energy drain too great. The Winchesters finally leave and Bobby has to go with them because of his connection to his flask.
The brothers go to the house and look around but find no sign of any inhabitants. However, Bobby is able to see the dozens of spirits trapped in the house. All of them ignore him, but one of them, Whitman Van Hess, tells the hulking ghost, Dexter O’Connell, that he shouldn’t have done what he did band warns that if he does it again then there’ll be consequences. Meanwhile, the Winchesters scan for EMF readings and pick up dozens of traces. When Dean tries to call Annie again, they hear her phone ring and find it lying on the floor.
Annie finds Bobby and can see him, and he realizes that she must be a ghost as well. He wonders if she avoided her reaper and she admits that she never saw one, and is surprised that Bobby was able to escape his. Bobby explains that he had unfinished business as the ghosts of Debbie and Dudley walk by. Annie tells Bobby that Dexter came after her and somehow she died, and then she discovered she was a ghost. When she wonders what they can do, Bobby admits that he doesn’t seem to be able to summon the energies necessary to move anything solid.
Dean and Sam figure that the place must be haunted with any number of ghosts, but are unable to find any traces of murders. When they check Annie’s voice mail, they discover that a spirit apparently left her a warning message.
One of the ghosts, Haskel Crane, comes into the lounge, picks up a book, and goes to the bar. Bobby tries to pick something up again and Haskel chuckles, deriding him as a novice. He explains that he was stabbed to death eighty years ago, but refuses to say who killed him. As he starts to leave, Annie asks him for help and he tells them to start small. Neither one of them can move a candlestick and Haskel tells them to release their frustrations, focus, and tell the object what to do. Bobby still isn’t able to do it and Haskel tells him that the alternative is to release his rage, but he doesn’t think Bobby can do it. One female ghost charges at Bobby, screaming, and then disappears, and Haskel explains that eventually all of the ghosts run out of energy and dissipate.
The Winchesters continue their search but are still unable to see Annie and Bobby. As the brothers leave the house, Annie notices a female ghost, Victoria Dodd, watching her. She talks to the ghost and realizes that Victoria was the one who tried to leave a voice warning. Victoria asks Annie to free them, but is interrupted when Bobby suddenly disappears.
Outside, Dean drinks from Bobby’s flask, and Bobby is pulled back to his tether. They find a flyer in Annie’s car for the Bodega Bay Historical Society and drive there to talk to the curator, Quentin. While Bobby tries to move objects and fails, Quentin explains that the Whitman’s fortunes were never good and he had to use the house as a bordello. The owner also took on a convict, Dexter, as a groundskeeper. However, Dexter killed Whitman’s fiancée on the eve of their wedding. Quentin tells them that Annie was there earlier and asked the same questions, and he tells them the same thing that he told her, that the house isn’t safe.
Sam and Dean go back to their motel room to go over the old files and discover that Dexter subsequently killed several of the prostitutes at the house. He was captured and convicted, but escaped, went back to the house, and was shot to death. While Sam wonders why Dexter would have gone back, Dean takes a shower and Bobby focuses on the steamed-over mirror.
Two of the dead teenagers’ friends, Brian and Jesse, go to the Van Ness House to make a video commemorating their friends’ death.
Dean gets out of the shower and discovers that someone has written the words “Annie trapped in house” on the steamed-over mirror. He calls Sam in and demands that the ghost show themselves, and Bobby turns on the faucets and writes “Bobby” in the mirror.
Jesse and Brian enter the Van Ness House and the door slams slam shut behind them.
Dean figures out that Bobby is still with them as a ghost and connected to a flask, and he and Sam head back to the Van Ness House to find Annie.
Dexter appears in the hallway and tells Brian and Jesse that they shouldn’t be there. However, as he charges at them, Whitman steps out and orders him to stop. Dexter does so, but when the teenagers thank Whitman, he thrusts his hands into their chests, killing them. Annie watches from the shadows as Whitman reminds Dexter that he told him to stop warning his victims. Dexter objects and Whitman concentrates and then destroys the former groundskeeper, causing him to burst into a glow of golden light. Once Whitman leaves, Annie tries to grab their camera without success. Victoria comes in and Annie asks the more experienced to help. The dead prostitute refuses, explaining that she and the other ghosts are afraid of Whitman, who killed all of them and tortures them for his pleasure. She doesn’t know where Whitman keeps their bodies and warns Annie that no one dares follow Whitman for fear that he’ll capture them. Annie insists that she has to destroy Whitman and Victoria reluctantly picks up the camera. When Whitman comes back, they’re forced to leave and the ghost killer hauls the two teenagers through a secret panel in the wall.
Dean and Sam equip themselves and go into the house, unaware that Bobby has grabbed his flask from out of Dean’s coat pocket. He goes off on his own while Victoria drops the camera near the Winchesters. They play back the video and see Annie on the tape, trying to warn them.
Bobby finds the two women and Annie asks Victoria to appear to Sam and Dean since she has more experience as a ghost. She reluctantly agrees and tells them that Bobby and Annie are there and that Whitman is threatening all of them. However, Whitman appears and destroys Victoria and then disappears. Realizing that they need to salt and burn Whitman’s bones, the brothers leave for the cemetery, unaware that Whitman has slipped his key into Sam’s pocket. Bobby and Annie can only watch as the invisible Whitman gets into the car with the brothers as they drive away.
Once Whitman is gone, Annie suggests that they take advantage of his absence to search the house and find the bodies. When they go to Whitman’s room, they discover that he burned Victoria’s body, destroying her. When Annie mentions that the house was a speakeasy during Prohibition, he figures that there must be a secret passageway and soon locates the switch. Inside are all of Whitman’s victims... including Annie. She stares at her own corpse and wonders what happens to ghosts when they finally pass on. Bobby figures that they just disappear, and Annie admits that she believes the same thing. She admits that she didn’t have any real life outside of hunting and that she’s ready for some peace even if he isn’t. Annie asks Bobby to give her a hunter’s funeral pyre so that she can rest in peace as well.
As Sam and Dean drive to the cemetery, Whitman tries to take control of the car and crash it. Dean manages to pull it over before they crash and the brothers get out. The Winchesters realize that Whitman must have planted a personal belonging on one of them and Sam find the key just in time. As Whitman attacks him, Dean yanks the key away, drops it on the ground, and shoots it. Once the key is destroyed, Whitman is “snapped” back to the house where his body is. They realize that Bobby and Annie are in danger and continue to the cemetery.
Whitman returns to his room at the house and realizes that Bobby and Annie were there. They’ve ducked out but he easily finds them and grabs Bobby. However, as Bobby starts to glow as he dissipates, the Winchesters burn Whitman’s bones at the cemetery. Whitman’s ghost flares into light and disappears as Bobby collapses, stunned unconscious. Later, Bobby wakes up as Sam and Dean come in. They can see him now and Bobby tells them that Annie is there as well. When they wonder how Bobby hung on, he shows them the flask and Sam realizes that he couldn’t contact Bobby because the flask was never present when he tried. Bobby explains that he stayed because they need his help and leads them to the secret room.
Sam and Dean burn the bones of all of the victims, including Annie, and Bobby admits that he’ll miss her. Dean drinks in her honor and then asks Bobby what he was thinking, giving up Heaven for them. Bobby insists that they have important work to do, but Dean says that what he’s doing isn’t right. Disgusted, Bobby disappears and the brothers drive off. Sam isn’t sure what to do but Dean is sure that whatever is going on, it’s not part of the natural order of things. As he warns that it won’t end well, Bobby sits unseen in the backseat and listens.