A woman, Sheila Case, is jogging down by the docks when she sees the image of an old-fashioned clipper ship in the harbor. It fades away in the storm and she goes home to take a shower. A shadowy figure appears behind her but when she turns to investigate, nothing is there. She goes back in and the figure materializes inside the shower and kills her.
Sam and Dean are driving through the night when Dean wants to know why a bullet is missing from the Colt. Sam explains that he shot the Crossroads Demon and someone else holds the contract on Dean's soul.
Sam and Dean then talk to Sheila's aunt, Ms. Gertrude Case, who reveals that her daughter apparently drowned in the shower, and she's working with someone known as Alex. She's also sexually interested in Sam, much to Sam's discomfort. After they leave, Sam reveals that there have been reports of people suffering from dry-land drownings after seeing the clipper ship. They find the Impala gone and "Alex" responsible: Alex is Bela Talbot, who has had their car towed. She's working with Ms. Case, apparently on an unrelated matter, but knows about the clipper ships.
A man is shaving bath when he catches a glimpse of a shadowy figure and finds his bathtub filled up to the brim. A hand reaches out of it and drowns him, filling his lung with water.
The next day, the guys interrupt Bela as she talks to the dead man's brother Peter Warren and send her off, then confirm that he and his brother both saw the ship while night diving. Sam and Dean have to make a hasty exit when Bela reports them to the police. Later she confronts them as they load up after recovering the Impala, and they spar over her motives over their's.
That night, Sam and Dean watch Peter but he spots them and drives off. His car grinds to a halt and the one-handed figure appears in the car next to Peter and he starts spitting out water. Dean shoots it with rock salt, driving it off, but Peter is dead. Sam is depressed, feeling that he hasn't saved anyone recently.
The next day Bela comes to visit them with information on the ship, and the sailor who was killed after his hand was cut off and made into a Hand of Glory, a mystic relic. Bela suggests they destroy the ghost but she wants the hand, which is at a maritime museum. She convinces Dean to accompany her to the black-tie affair, while Sam accompanies an amorous Gertrude using her invitation. Bela fakes a faint so Dean can get her upstairs past the security guards. While Sam tries to fend off Gertrude's advances, Dean goes for the case holding the Hand of Glory and Bela fakes her and Dean making out to keep the guard out. However, Dean runs into the guard outside, and the guy figures Bela is with someone else.
Dean shows Bela the hand and she's clearly interested in it but Dean holds on to it. Meanwhile, Gertrude asks about Peter's death and notes that the Warren brothers killed their father, and that Sheila was involved in a car accident that resulted in her brother's death. Dean and Bela arrive and Bela gets Gertrude away while promising to meet them at the cemetery later. They get to the car only to realize that Bela has taken the Hand. She's waiting at the dock… and sees the clipper.
Dean is griping when Bela visits them to explain she had a buyer set up for the Hand and needed them to provide cover. She's already got rid of it, and now she figures she's next to die. Dean and Sam have figured out that the captain who hung the ghost was the dead man's brother. Now the spirit goes after those who have spilled their own family's blood. She refuses to tell them who she killed, even in return for their help. They agree to help her anyway, going to the cemetery and performing a ritual. A storm kicks in and the ghost appears, throwing away Dean and causing Bela to choke. Sam continues with the ceremony while Dean tries to help Bela. Sam completes the ceremony and the ghost's brother appears. The ghost attacks his brother and they disappear in a burst of water.
Bela pays off Sam and Dean for their help, rather then thank you. Dean drives them toward Atlantic City and thanks Sam for doing what he did. He figures Sam will go on without him, but Sam isn't hearing it. Sam is concerned about Dean and wants him to start being concerned as well, but Dean would rather play craps.