The episode opens with Locke reading a file on someone. He throws the file into a fire and shouts for someone to stop shouting, no-one can hear him. We flash back to Locke seeing his father on the island for the first time. Ben says that Locke brought him here. He says to be careful about getting too close to him. Locke goes to take off his gag, to find out how he got there when Anthony Cooper bites Locke's hand. Tom tazers Cooper and he lets go. Locke's hand is bleeding. Ben asks Locke if he would like to go with them, and Locke says yes. Ben says that they are holding Kate a few buildings over, he can say goodbye.
On the island, Kate isn't comfortable sleeping in a tent that isn't hers. Sawyer says that he will go to her tent then, and Kate says that she wants to be alone, it's old habits. Sawyer offers to walk her home, beside, he needs to pee. Sawyer sees Hurley and Jin asks what they are doing. They ask what he is doing and he says he needs to go pee. Hurley says that's what they are doing too. Sawyer goes into the jungle when he hears a rustling. It's John. Sawyer has his gun ready. He asks what he is doing there, and Locke says he has come to see him. John says that he kidnapped Ben, and he wants Sawyer to kill him. Sawyer says that John should kill him if he wants him dead. John says he isn't a murderer, and Sawyer says neither is he. John asks about the man he shot in Sydney, and Sawyer says the others must have gotten their facts wrong. John starts to walk off, and Sawyer follows him.
John flashes back eight days ago. He is helping Cindy tie up a tent. People are staring at John. Cindy tells him that they are excited that he is there, they've been waiting for him. Tom comes for Locke; Ben wants to speak to him. At Ben's tent, Ben is listening to the tape that Juliet made about Sun. Locke asks what the tape recorder is. Ben says that Juliet is gathering information for the Others. She is finding out who is pregnant on the island and they are going to take them all. Locke looks uncomfortable at this and Ben says that he shouldn't worry, they've done it before. Ben tells Locke that he isn't ready to know about the island yet, because he is still stuck down by the thought of his father. Ben has been walking because Locke being near has helped him. Ben says that John needs to kill his father to release the hold his father has on him. Locke asks to see the magic box, and Ben says that it is a metaphor. He can't show Locke anything unless he shows his commitment to the Others. We see Anthony Cooper tied to a post.
At the beach, Charlie is packing food into a suitcase. He says that they got back early that morning. Jack says next time they go out they should sign him up. Charlie brings the food to Desmond, and says that they should tell Jack. Desmond says that they shouldn't; Jack might not be trustworthy, especially in the presence of Juliet. They find it a good idea not to tell him and decide that they have to tell someone they can trust. In the jungle, Sawyer is in pain from lack of shoes. Sawyer asks about the file they have on him. Locke says that it said his parents died, but it didn't tell him why his father shot his mother, and turned the gun on himself. Locke says it must have been hard. Locke then says it had high school transcripts, criminal records for all the con jobs. He guesses that is why he uses an alias. Sawyer takes the gun out of his pocket and knocks Locke to the ground with it. Sawyer asks where he is taking him. Sawyer asks why is he getting him to kill Ben, and Locke says it's because he can't. Sawyer lets John get up. At the beach, Hurley gets Sayid to look at Naomi. They go in, and Sayid asks her who she is. She says that she was doing a rescue mission for Desmond. She took off from a ship, 80 miles north. She says that the full wreckage of Oceanic 815 was found off the coast of Bali, four miles deep. They sent robots down and found that all the bodies were on board. She thought it was a fools errand to find him in the middle of the ocean, but when she got to the coordinates, an island appeared when the clouds cleared. The instruments started spinning and she realised that she was going down, so she grabbed a parachute and bailed out. He questions her more, he doesn't believe her. She hands him the satellite phone, and she says to remind her not to rescue him.
Locke and Sawyer continue walking. They get to a stream, and Sawyer dips his feet in. John flashes back to three days ago. Ben wakes him up and takes him to his father. They get there, and Ben gives him a knife; he wants Locke to kill him. The whole of the Others are watching, but John can't do it. Ben says that he must have made a mistake, Locke isn't special. John leads Sawyer to The Black Rock, the slave ship. Locke says that Ben is inside, in The Brig. They go in, and Locke says to be careful, there is dynamite in the crates. Locke lets Sawyer walk into the room, then he shuts the door and locks it. Sawyer shouts to John to let him out. The person under the cloak is screaming, and Sawyer says to shut up. He pulls off the hood and it is revealed that it isn't Ben, it's Anthony Cooper. Sayid fixes the radio, but he can't get a signal, there is interference. Kate finds them and asks them where they got it from, but Sayid says he will only tell her if she keeps it a secret. Sawyer is trying to get Locke to open the door, when Rousseau comes in. Locke asks Rousseau what she is doing there, and she says to get dynamite. He says to be careful, it's unstable. Locke flashes back to two days ago, his hand has healed. Richard, the man from Mittelos says that it's a nice view up there. He then tells Locke that Ben knew he wouldn't kill his father and that he did it to humiliate him. Locke says that he can't kill his father. Richard gives him Sawyer's file and he tells him that he is the man who can. Richard says that they aren't on the island for fertility research, there are much greater things on the island.
Sawyer holds the gun up to the door, saying that he will shoot if he doesn't let him out. Locke says that there aren't any bullets in the gun; Sawyer wouldn't have attacked him with his knife if there were. Cooper says that he guess he didn't raise a dummy. That bald headed bastard outside is his son. Cooper says that he is driving down the freeway when someone slams into the back of his car. He goes into the divider at 70 miles per hour. He gets put into the ambulance and one of the paramedics smiles at him. The next thing he knows he wakes up in a dark room, and when the door opens, he looks at the same person he threw out of a window. John Locke, his dead son. Sawyer asks if John died from the window, and Cooper says he survived the fall -- that it just crippled him. He died from the plane crash. Sawyer says that he was on the plane too, and it didn't crash in the Pacific, he crashed on the island. Cooper asks if he is sure that it is an island. Sawyer asks then what is it, and Cooper says it's a little hot for heaven. Sawyer thinks that he is crazy, but Cooper says that the plane was found, one minute he is in a car wreck, the next he is in a pirate ship. Sawyer asks why he threw Locke out of a window, and Cooper says that it was because he was becoming a nuisance. He conned him into giving him one of his kidneys and John never got over it. Sawyer says conned, and Cooper says yes sir. Sawyer asks his name. He says a conman goes by many names. He says a list, one name is Tom Sawyer. Sawyer asks about the name Tom Sawyer. He says he was young and Huck Finn was taken. James says how about that. Cooper says how bout what? James says, 'Sawyer's my name too.'
John flashes back again. The Others are moving. Ben says that they are going, they will leave a trail that he can track, but he can't follow unless he has his father's body on his back. Sawyer asks if Cooper has ever been to Alabama, and Cooper says yes. Cooper asks if he is his daddy, and Sawyer says no, but that he killed his daddy. Sawyer hands him the letter. Cooper reads the letter out loud. It's the same letter that a young James Ford wrote. Cooper says not to get worked up. Sawyer says his mothers name. Mary. Cooper remembers her. He says she begged him to take her $38000 and rescue her from her sorry little life. Sawyer tells him to finish the letter, but Cooper rips it up instead. Sawyer runs at Cooper, and wraps a chain around his neck. Sawyer says, 'you wanna go to hell,' and he chokes him to death. Locke opens the door, sees his father's body, and says thank you to Sawyer. On the beach Kate says she needs to talk to Jack in private. Jack says that anything Kate wants to say to him can be said in front of Juliet. Kate says that Naomi crashed on the island and she can rescue them. Kate says that nobody told him because they don't trust him. Jack asks how she is to contact her boat, and Kate says that she had a phone radio. Juliet says that they should tell her, but Jack says no.
At The Black Rock, Sawyer is being sick. John said that he ruined their lives, he had it coming. He tells them that Juliet is a mole, she was sent to find out which of their women were pregnant, and then they are going to take them. Sawyer says that they won't believe him, but then Locke says that they will. He hands him the cassette player, and then he walks off. He grabs Anthony Cooper's body, and he sets off to find the Others, he isn't going with Sawyer.