Roger Linus carries his newborn baby and his wife, Emily, who has just given birth and is dying, to the closest road and flags down a passing car. Horace and Olivia Goodspeed stop and offer to take them into town when Emily tells Roger to name the baby Benjamin, and then she dies.
WHOOSH to the island, were Alpert asks Ben if he wants the tape recorder with instructions for Juliet taken back to the medical station. But Ben thought Alpert already took it. He goes outside to ask Tom about it and sees Locke walking into their camp carrying the body of his father. Locke reminds Ben that if he killed his father, Ben would tell him everything about the island. Locke throws the body down and suggests Ben start at the beginning.
Ben tells Locke that he isn't the leader of their community. Everyone answers to someone, and Ben answers to Jacob. Locke then wants to be taken to Jacob, but Ben can't do that. Jacob will only talk to be Ben. Ben was born on the island and everyone else was brought there. Jacob trusts Ben and tells him what to do. No one else has even seen him. Locke thinks Ben is lying but makes Ben take him to Jacob anyway.
Flashback to Roger and an eleven year old Ben arriving to the island and being greeted by Horace Goodsped. Roger thanks Horace for the opportunity. Roger and Ben are taken to processing where they watch a welcome video with Dr. Marvin Candle, and then Roger is given his job assignment: workman. Roger is not happy about it. He thought he'd be helping to change the world, not clean up after everyone. But that is his only option. He has no choice, and he begrudgingly accepts the position.
Young Ben goes to Dharma school. Their teacher, Olivia Goodspeed, is giving a science lecture when KA BOOM! There's an explosion in the distance. Air raid sirens start to wail, and Olivia tells everyone to take their positions. Young Ben is scared, but his friend, Annie, tells him it's the hostiles. They'll be okay, and she holds his hand. That night, young Ben overhears his dad arguing with Horace about the attack. Roger is mad and drunk. He says this isn't what he signed up for, and he wants another thirty grand for hazard pay. Horace reminds Roger that he did him a favor and Roger kicks Horace out.
Ben hears a tapping on his window. He looks over and sees his dead mother staring back at him! Young Ben stumbles backwards, and when he looks up again she's gone. Later, on his birthday, young Ben comes home and finds Roger passed out in his chair surrounded by empty beer cans. Ben takes his father's boots off and Roger wakes up. He sees an unwrapped box given to Ben and realizes he forgot Ben's birthday. Roger apologizes, saying it's hard to celebrate the day Ben killed his mom. He and Emily were out on a hike, but Ben just had to come two months early. Now Emily's gone and he's stuck on this island with Ben. The words cut deep, and Ben runs off crying. He runs through the jungle and sees his mother again. He runs towards her, but she's on the other side of the pylon fence. She stops him from crossing the boundary, telling him it's not time yet, then disappears back into the jungle.
WHOOSH to the beach camp, where Sawyer returns a changed man. He finds Sayid, who asks what happened to him. Sawyer says it doesn't matter. He gives Sayid the tape recorder proving that Juliet is a mole. They immediately go to Juliet's tent, but she's not there. Kate tells them she left with Jack right after she told them about Naomi. Sayid is not pleased that Kate told Jack about Naomi, and they play the incriminating tape for her.
Ben and Locke trek through the jungle to see Jacob. They reach a break in the trees. On the ground is a line in gray ash that encircles the area in front of them, and in the center is a cabin. Ben says, "We're here."
Flashback to young Ben in a clearing at the pylon fence. He enters a code into a pylon keypad, and disarms the fence. Ben runs into the jungle looking for his mom and meets Richard Alpert. Young Ben tells Alpert she's dead but she's here and she talked to him. Alpert believes Ben and asks what she said. Ben tells him she said that he couldn't go with her. It wasn't time yet. This seems to have great significance to Alpert. Ben wants to go with Alpert, but he says no, he can't. Alpert tells him to go back to his people. Young Ben says he doesn't want to go back. He hates it there. Alpert tells him if that's what he really wants go back, think about it and be patient.
WHOOSH to Ben and Locke step onto the porch of the cabin. It's creepy. Ben tells Locke to turn off the flashlight. Like Locke, Jacob doesn't like technology. Ben lights a lantern. He announces out loud that he's there with Locke, and they enter the cabin. It's dark. Inside is a small stove, a table and a chair, but it's empty. No one is there. Ben talks to the chair and introduces Locke. Locke is confused. Who is Ben talking to? Ben says Jacob is sitting right there. Can't Locke see him? Locke says no. Ben says he knows someone is there and that Locke is too limited to see. Locke turns to leave, and then he hears a voice. "Help me." Locke asks Ben what he said, but Ben didn't say anything. Locke turns on his flashlight then BOOM! Everything goes crazy! The cabin starts shaking, a window shatters, the lantern falls and starts a small fire. Locke is knocked to the ground and drops the flashlight. As the beam of light rolls around, Locke sees what looks like Ben struggling with someone. Locke scrambles out of the cabin and runs into the jungle. Soon Ben emerges. Locke asks what was that? Ben says that was Jacob.
At the beach camp, everyone is crowded around Naomi. They all have just been told about her, and they question why she was kept secret. Sayid says Naomi represents their best chance of getting off the island, and they wanted to keep it safe from Jack. He believes Jack is one of them now. Sawyer plays the tape, and they hear the last message Juliet recorded for Ben about Sun's pregnancy. They are shocked. Right then Jack and Juliet return. Juliet tells Sawyer to turn the tape over and play the other side. He does, and they hear Ben's message in response. He reveals their plan of invading the camp and taking the women. Juliet confesses that she told Jack what Ben was making her do after she performed Sun's ultrasound. Jack tells the group he hasn't figured out a plan yet, but they have some catching up to do.
Ben and Locke head back. Locke insists there is no Jacob, that Ben is a fraud and it's time he told his people the truth. Ben says yes, some of the things he said were not true. Like him being born on the island. Locke asks where he come from then.
Flashback to adult Ben getting ready for work. He's a janitor just like his dad. Roger picks him up in a blue Dharma VW van, and they drive off. Ben mentions it's his birthday. Roger suggests they head up to the Mesa and drink some beers; have a little father and son time. Ben asks if Roger really blames him for his mother's death. Roger shrugs. Ben keeps looking at his watch, and Roger asks why. Ben says he missed his mom as much as Roger did, but the difference is he's had to put up with Roger and that required a tremendous amount of patience. Ben says good bye and pulls out a gas mask and a canister. He puts the mask on and opens the canister. Soon he sees a trickle of blood leak out of Roger's nose. Roger suddenly jerks in pain. Ben calmly watches from behind the gas mask as his father flails, shudders and finally dies. Ben gets out of the van and walks back to the barracks. And there, scattered everywhere, lie bodies. All of the Dharma Initiative members are dead. Ben sees Alpert come out of the jungle along with the rest of the Others. Alpert gestures to them, and they begin collecting the bodies.
WHOOSH back to Ben and Locke standing over a mass grave where the Others dumped the bodies of the Dharma Initiative. Ben tells Locke that these were his people. They came seeking harmony but couldn't even coexist with the island's original inhabitants. Ben says when it became clear one side had to be purged, he did what he had to do in order to survive. He was smart enough not to end up in this ditch and that makes him considerably smarter than Locke and then he shoots Locke. Locke pitches forward and tumbles into the mass grave. Ben asks what Jacob said to him. Locke tells him. Ben says he certainly hopes Jacob can help him, then he turns and walks away.