The episode begins with a flashback to the 1950s, where John Locke's birth mother is revealed to have been a teenager who was dating a man twice her age, much to the anger of her mother. On a rainy night, Emily runs out screaming at her mother and gets hit by as passing car. She is taken to the hospital, where she mentions that she is pregnant, causing the hospital to go in to a frenzy as they try to deliver the child. The child is born, and whisked away as it is premature - the mother upset at her child being taken away exclaims that his name is John. A few days later the mother (Emily) is seen with her mother, and regrettably gives the child up for adoption. A man is seen behind the glass of the hospital room, clearly interested in the child but not directly related. Emily's mother mentions that she has no idea who the man is, although it appears that she may have had some interaction with him.
A few years pass, John is approached by the unknown man (Smiley?) and is given a test where he is to pick out items that belong to him. John at first seems to pass, but picks up a knife much to the disinterest of the man, who claims to be testing Locke for a special school admittance. The man gruffly tells John that he failed and that the knife was not his, and leaves.
Back to the present, Sayid and Desmond witness the captain and one of his men arguing and fighting over how Ben could have known his identity. The fight continues and Michael, who has been helping Ben by spying on the freighter, is attacked by one of the men, and is almost killed when the gun locks causing it not to fire. Meanwhile on the island, Locke, Ben and Hurley set out to find the cabin not realizing each had been following the other. Upon realizing that they're lost, John Locke decides that they should settle to camp where they are. He has a dream in which he is told to find a Dharma Initiative member named Horace, who was building a cabin for him and his wife and reveals that he is dead. He tells Locke to find him (Horace) and then to find someone he refers to as 'him'. Locke awakens to see that Ben is watching him and has noticed that he is dreaming, the 3 set forth to find the cabin based on the location of the dead bodies that Ben had buried in a shallow grave, and where Ben had left Locke to die after shooting him at the end of season 3. They find the cabin, and Ben tells Locke that he will not enter because the island has rejected Ben, and now is the time for Locke to embrace the island since it seems to desire him more. Hurley out of fear and disgust remains with Ben, leaving Locke to enter the cabin - where he finds Jack's father and Kate (Jack's step-sister). Locke is confused but finally asks him how to save the island, at which point a long and awkward pause occurs. Locke leaves the cabin, having been told what to do to save the island, that is to 'move the island'.
On the freighter, the captain has been shot, and a few men are assembled to take the island by force and to kill everyone. Sayid obtains a boat with the help of the captain and sails back to the island to rescue anyone he can. The men approach the island, where upon a transceiver indicating the location of the men is disabled on a GPS system was dropped for Jack and those with him to find and follow.