This Locke-centric episode opens with Locke in the Black Rock as he is reading a folder which he promptly burns. We can hear someone (his father, Anthony Cooper) making noise in the brig, a room behind him, and Locke tells him to keep it down. Later, Locke arrives at the beach camp and asks for Sawyer’s help. He tells him that he has infiltrated the others and kidnapped Ben and that he wants Sawyer to kill him. Sawyer refuses at first although he does eventually follow him. Sawyer thinks that Locke is trying to con him, but Locke tells him that he is not conning him, he wants him to kill Ben because he can’t do it. Sawyer tells him that he will go to where Locke has Ben but that he isn’t going to kill him, he is going to bring him back to the main camp, but Locke says that he will change his mind. When they reach the Black Rock, Sawyer (and we, I think) sees the slave skeletons for the first time, something that we won’t get any information on until the final season.
When Sawyer enters the brig, Locke locks him in there and Sawyer realizes that the man Locke kidnapped is not Ben. Rousseau shows up to pick up some dynamite and asks about the noise coming from the brig, but Locke doesn’t tell her anything and she leaves with what she came for. Cooper tells Sawyer that he the last thing he remembers before reaching the island is crashing his car and being treated in an ambulance. The next thing he remembers is staring at the man he threw out a window, his dead son, John Locke. Sawyer asks if he was dead because he threw him out the window and Cooper informs him that Locke survived the fall but was paralyzed and that he died because his plane crashed in the Pacific. Sawyer tells him that he was on the same plane and that they didn’t crash in the Pacific, they crashed on the island. Cooper asks if he is sure it’s an island and when Sawyer asks what else it would be he says “It’s a little hot for heaven, isn’t it?” This was a popular theory for a long time, that they were actually in hell, but as we all know that’s not the case (which wouldn’t have been all that much fun). After telling Sawyer about the plane being found on the bottom of the ocean, he mentions that he conned Locke into giving him one of his kidneys and Sawyer’s interest is piqued. He eventually realizes that this is the man responsible for his parent’s death and the man whose name he eventually took. He makes him read the letter, but before finishing it, Cooper rips it up and Sawyer chokes him to death with one of the chains in the brig.
Sawyer vomits after killing Cooper and Locke tells him that he can go back to camp. Sawyer asks Locke why he did this and Locke says that it’s because he ruined both of their lives and that he had it coming to him. Locke tells him that Juliet is a mole and gives him the tape in which she explains who is pregnant, etc. He also tells him that he is not going back to camp with him and that he was never undercover with the others. He says he is on his own journey now and when Sawyer asks if what Cooper said was true (about him being thrown out a window and paralyzed) Locke says “not anymore” and picks up his father’s body and heads off after the others.
At the beach camp Charlie and the other people who know about Naomi debate about whether or not to tell Jack about her, but most of them feel that he cannot be trusted. Hurley eventually tells Sayid about Naomi and brings him to her. Sayid is able to get Naomi’s satellite phone working although there is a signal blocking the ability to use it. When Kate sees the sat phone, Hurley tells her they found it in the luggage, but Sayid is willing to let her in on what is going on. Later, Kate tells Jack about Naomi and that no one trusts him. Juliet tells Jack that they should tell Kate something, but Jack insists that the time is not right.
The flashback consists of what has happened to Locke since he joined up with the others and found out his father was on the island. While setting up camp with the others he is told by Cindy (the stewardess) that everyone has been waiting for him. In a meeting with Ben he is told that in order to find out everything he wants to know about the island he will have to kill his father in order to release the hold his old life has over him. When he is brought to his father, however, he cannot kill him and Ben tells everyone that Locke is not who they thought he was.
We see Richard speak with Locke and let him know that Ben knew he wouldn’t be able to kill his father. He tells him that the other got very excited when they found out someone on the plane was paralyzed but gained the ability to walk again after landing on the island because that could only happen to someone very special. He also says that Ben has been wasting their time with researching things like fertility and that the others have been waiting for someone special to come along and remind them that they are all there for something more important. He clearly thinks that Locke is that person and he wants him to find his purpose, but in order to do that his father needs to be killed. Since he knows that Locke is unable to kill him, he gives him a folder with information about someone who will (Sawyer). Something fun to think about is that we find out next season that Richard has been watching John Locke grow since he was a child based on what he is told by Locke himself (actually MiB if I remember correctly) in the past.
The final flashback shows the others pack up and leave Locke behind. Ben tells him that they will leave a trail that he can track, but says that he shouldn’t bother following them unless he is carrying his father’s dead body on his back. Clearly this is how he ended up in the main scenario of this episode.