The episode begins with a woman giving birth outdoors in what, at first, appears to be the island. The baby is born, but the woman, Emily, is in pain and bleeding heavily. Her husband, Roger, carries her and the baby through the forest to the roadside where a car soon stops and a man and woman quickly jump out to help them get to the hospital. Just as they are about to get them in the car, Emily tells Roger to name the baby Benjamin, and she dies.
At the Others' new camp, they appear somewhat shocked that Locke arrives carrying his father's body on his back. Locke meets with Ben and demands that he take him to see the mysterious Jacob, but Ben tells him that is impossible. Soon after, Mikhail is shown racing through the jungle like a madman. He stumbles into the camp, yells for Ben, and tells him about Naomi and the satellite phone she carried. After receiving some strange stares, Mikhail claims the sonic defense system's power was not set strong enough at the time to kill him. Locke says Ben can't deal with that issue at the moment, because they are on their way to meet Jacob. Ben is forced to take Locke after he beats Mikhail unconscious while several of the onlooking Others do nothing to intervene.
In flashbacks, a young Ben and his father arrive at the Island as part of the DHARMA Initiative. He is educated with other children in the Initiative, one of whom became his good friend Annie. During one day the "hostiles", "natives" of the Island, attack the camp. Later in the flashback, Ben sees a vision of his dead mother on the island, which prompts him to sneak into the forest in search of her. While Ben is in the forest calling for his mother, he encounters Richard Alpert, one of the "hostiles". Richard tells Ben to not be afraid, and asks him if he is lost. The young Ben says that he is looking for his mother, and tells Richard that he does not like the DHARMA Initiative, and wants Richard take him to their camp. Richard tells Ben that if he really wants this, that he must be patient, and wait for his time to come. Ben listens to Richard and returns to the DHARMA Initiative.
At the survivor's camp, Sawyer plays Juliet's tape for Sayid. They visit Juliet's tent only to find that she and Jack are both missing. Kate shows up and begins to defend Jack. With a look of disgust, Sayid walks away and tells Sawyer to play her the tape. Later that night, all the survivors are introduced to Naomi and the tape is played for all to hear. Just then, Jack and Juliet return to the camp. Juliet tells Sawyer flip the tape over and play the other side, which is Ben's plan to kidnap Sun and other pregnant women. Jack reveals that he knew of this for some time, but that he had kept it secret because he did not know what to do about it yet.
Ben and Locke arrive at Jacob's "house". The two of them slowly enter and walk up to a seemingly empty chair. Ben begins to talk to where he implies Jacob sits, but Locke cannot see anyone. Ben insists that Jacob is sitting in the chair right in front of him. Locke, growing frustrated and angry, tells Ben that the chair is empty, and that he is crazy and pathetic. Just as Locke is about to exit the house, a deep voice says "Help me". Locke pulls out a flashlight, which Ben had warned him not to do (saying that Jacob "dislikes technology"). Suddenly, objects in the room begin to violently fly about and windows shatter, Ben is flung against a wall. Briefly, the shot of a strange man sitting in the chair facing Ben is seen on screen. Locke runs out of the house and Ben exits soon after, clearly quite shaken up. Locke still doesn't believe Jacob is real, and thinks that Ben was just "putting on a show" for him. The two men begin to head back to the camp.
In another flashback, we see an older Ben at the barracks, on his birthday yet again. He is helping his father load a blue van. His father has forgotten his birthday yet again, but once Ben reminds him, he tells him that they will go do "father and son things" once they've finished their work for the day. They drive the van up to a hill and Ben asks his father if he really blames him for the death of his mother. Roger refuses to answer him, and Ben finally snaps after years of neglect and abuse. He pulls out a gas mask and tells his father goodbye before filling the van with a toxic gas that kills his father. Ben returns to the barracks where all of the DHARMA workers are dead. Alpert and his men emerge, and it's revealed that they were working with Ben.
On the island, Locke notices that Ben is leading him along a different path. Ben then admits to him that he was not born on the island, and that he wants to show him where he really came from. They arrive at a pit full of DHARMA member skeletons, and Ben tells him that he helped kill his own people. Then, in a sudden turn of events, Ben shoots Locke in the lower ribs, who falls into the pit. Ben demands to know what Jacob said to Locke, and he tells him, "He said... 'Help me!'" Ben replies back, "I hope Jacob can help you now, John!" Finally, Ben leaves, leaving Locke for dead.