In 43 AD
Claudia is in the ocean clinging to the remains of a ship she looks around and sees a magnificent tropical island. She is washed ashore and when she struggles to her feet her billowing red dress reveals her advanced stage of pregnancy. The beach is strewn with wreckage from a shipwreck. She makes her way inland and drinks from a stream. As she drinks she sees a woman reflected in the water. The woman takes Claudia to her primitive camp, feeds her and treats her injuries.
The woman answers Claudia's questions telling her that she is alone and that she also arrived "by accident". Eventually she says that every question Claudia asks leads to another question and she suggests that Claudia should rest. She won't allow Claudia to look for other survivors, saying that she will find them.
Claudia soon goes into labor with the woman acting as midwife. A beautiful boy Claudia names Jacob is delivered. Then another boy is born. Claudia says that she only picked one name. Swaddled in light and dark material the woman cares for the babies with concern. When Claudia asks to see the second boy, the woman kills her with a rock.
Thirteen years later
The young Man in Black finds a game on the beach. Jacob runs up and Boy in Black tells him it is a game and that he "just knows" how to play. He agrees to play with Jacob, but only if Jacob doesn't tell their mother as he believes she will take the game away from them.
Mother is working at her loom and she asks Jacob whether he loves her. He says he does and she says "Then tell me what happened". She joins the Boy in Black on the beach and he immediately guesses that Jacob told her about finding the game. Mother says that Jacob doesn't know how to lie. She tells him that he is "special". She says that it was she that left the game for him. The boy in black says that he thought it may come from "Somewhere else, across the sea." She tells him that there is nowhere else, that the island is all there is. When Mother says that her mother is dead the boy asks what is dead. His mother says that it is something he will never have to worry about.
The boys chase a boar but the boar is killed by three men hunting so they run home and demand an explanation from Mother. She says that these men are not like them because "we are here for a reason". Both boys insist on knowing what is the reason. Mother blindfolds the boys. She tells them that the other people are dangerous because they come, they fight, they destroy, they corrupt and it always ends the same. She tells the boys that she has made it so they can never hurt each other. They turn to see a cave with a stream running into it; the cave emits a glowing golden light. She tells them that it is the reason they are on the island. She tells them they must never enter the cave. The Boy in Black says that it is beautiful, she agrees and tells them that a little bit of the same light that is in the cave is inside every man but people always want more. Mother says that while the other people can't take it they might try and if the light goes out here it goes out everywhere. Mother has protected the place but when she no longer can then it will have to be one of the twins who protects it.
Some time after, the boys are playing Senet. The Boy in Black tells Jacob that he can't make a move because it is against the rules. He says that one day Jacob can make up his own game and then everyone will have to follow his rules. Claudia appears a short distance away, bathed in light but only the Boy in Black can see her - because, as she explains - she is dead. She takes the Boy in Black to a place on the other side of the Island and shows him a bustling settlement. She says these people came from across the sea thirteen years ago. She tells him that she is his real mother and Jacob's mother too and that he comes from across the sea.
The Boy in Black wakes Jacob up at night and urges him to come with him to join the people in the village. He tries to explain to Jacob that the people in the village are their people and that Mother lies about everything, that she doesn't love them and that "She is not even our Mother". Jacob cracks and beats the Boy in Black. Mother separates them as Jacob cries that his brother is leaving and going to the other people. The Boy in Black says he is going to go "home" across the sea and that she killed his Mother and that they don't belong here. He pleads for Jacob to come with him. Jacob chooses not to. Mother tells the Boy in Black that whatever he has been told he will never be able to leave the island. He says that one day he will prove that that is not true.
Jacob joins Mother on the beach. She admits to killing his real mother and explains that had she lived she would have taken the boys back to the bad people and that she needed Jacob to stay good. Jacob asks why she loved his brother more and she says that she loved each of them in different ways. Jacob agrees to stay with her.
Thirty years later
Jacob has finished a piece of cloth on the loom. Mother claims tiredness as she grinds herbs. Jacob observes his brother working at a project with the other people. They talk over a game of Senet. The Man in Black tells Jacob that Mother may be insane but she is right about his people being bad. He says they are greedy, manipulative, untrustworthy and selfish. He explains he stays with them as a means to an end, that is, that he is leaving. The Man in Black reveals to Jacob that he has found a way off of the Island. He throws the knife wildly and it adheres to bricks. He talks about the way metal behaves strangely at certain sites and this has suggested a way off the Island. The Man in Black asks Jacob to join him. but Jacob says that the Island is his home and he doesn't wan to leave. The Man in Black says that it is not his home.
Jacob tells Mother that The Man in Black has found a way to leave. Mother goes to see the Man in Black and sees that the other people have dug a well. She enters. The Man in Black complains how he has searched the Island and not once come close to finding the cave. He tells her that he then thought about another way to get to the light. He tells Mother that the people have some very interesting ideas about what to do with the light. She gives a look of alarm at the knowledge these people now have. He shows her he has found a way to dig into the light that exists beneath parts of the Island, He has constructed a wheel and he plans to dig a large hole into the light and use it and water to construct a mechanism which will allow him to leave the Island, because he doesn't belong there. He says with hatred that he knows all this because he is "special". Mother feigns a goodbye hug and while saying that she is sorry she cracks his head against the bricks.
Mother returns to Jacob and takes him to the glowing cave. She tells Jacob that he is going to protect it now. Jacob asks what is inside the cave and Mother says: "Life,death, rebirth, it's the source, the heart of the island." She asks him to promise that he will never go down there, that to do so would be much worse than dying. She pours some wine from a flask making an incantation as she does so. She says that in drinking the wine he accepts the responsibility of protecting this place for as long as he can and then to find a replacement. He is unwilling and saddened at being made her successor only by default, as she had always favored his brother. She admits she was wrong and that it should have been him all along. Jacob drinks.
The Man in Black wakes. His well is wrecked and filled in and he sees smoke afar. He finds the village destroyed and his people dead. Jacob and Mother return and Mother says a storm is coming. She sends him for firewood and asks him to be careful but does not reply when he says that he will see her back home. At Mother's camp the loom is wrecked and the camp in disarray. Mother finds the game she had left for the boy in black thirty years before. As she holds the black playing piece she is run through from behind by the Man in Black's dagger. With tears in his eyes the Man in Black addresses her as "Mother" and asks why she let him live. As she dies she says: "Because I love you. Thank you."
Jacob returns and sees what his brother has done and attacks him as he did as a thirteen year old. He drags his brother through the jungle. The Man in Black reminds him that Jacob cannot kill him. Jacob replies that he has no intention of killing him. He brings him to the glowing cave and throws him down the stream towards the mouth of the cave. The Man in Black is sucked into the source. Moments later The Smoke Monster bursts from the cave and disappears into the jungle. Jacob washes himself at a stream and sees his brothers body lying nearby. He hugs him tearfully. Jacob carries his body back home and finds the two jewels and places them in a pouch. He lays Mother and the Man in Black's bodies' side by side with the pouch at his mothers camp.
Centuries later, Jack Shephard and Kate Austen discover the two corpses laying side-by-side in the cave, as well as the two stones. John Locke dubs the pair "our very own Adam and Eve."