- Claudia washes up on the island, shipwrecked and very pregnant
- Mother helps her give birth to twin boys
- Mother kills Claudia and raises the boys as her own
- Mother tells Jacob and the Boy in Black the island is the only place in the world
- A 13-year-old Boy in Black finds a senet game and teaches a 13-year-old Jacob how to play it
- Hunting boar, Jacob and his brother discover other people living on the island
- Claudia appears to the Boy in Black and tells him she is his mother and the other people on the island are his people who shipwrecked there
- The Boy in Black leaves to go live with his people and find a way off the island
- 30 years later, Jacob discovers the Man in Black and his people are digging wells trying to find a way to leave
- Mother knocks the Man in Black unconscious and kills all the people in his village
- Mother performs a ceremony and Jacob becomes the protector of the island
- The Man in Black regains consciousness, sees what Mother did, and kills her
- Jacob throws the Man in Black into the heart of the island and creates the smoke monster
- Jacob leaves the bodies of his mother and his brother in the caves
A young woman, Claudia, clings to a jagged piece of boat hull as the waves carry her ashore. She gets up, and we see that she's very pregnant. Claudia is sunburned, parched and dazed. She wears a toga-like gown that's wet and ragged, and she's got a bad gash on her leg. She stumbles into the jungle and finds a stream, gulping the fresh water — and sees a reflection in the stream of another woman. The other woman looks to be in her late 40s and wears worn, hand-made clothing from an undetermined distant age. She speaks Latin to Claudia and offers to help her. Claudia thanks her.
The woman takes Claudia to a cave where she lives. Claudia asks where the rest of the woman's people are, and the woman says she's alone. Claudia is concerned about the other people on her ship. She needs to go find them. The woman comforts Claudia and says if they're on the island, she'll find them. Just then contractions wrack Claudia's body and she goes into labor. The woman helps Claudia give birth to a son, whom Claudia says she'll name Jacob. But it isn't over — there's a second baby, another boy. The woman swaddles Jacob in light colored rags and the second baby in darker rags. Claudia is excited but weary. She says she only picked one name. She asks to see the second baby, but the woman picks up a rock and slams it down on Claudia's head, killing her. The babies cry, and the woman cradles them lovingly. This is Mother, and welcome to the origin story of Jacob and the Man in Black.
A 13-year-old Boy in Black finds a wooden box on the beach. He turns it over and hears something rattle inside. Excited, he takes the box and runs into the jungle. It's an ancient senet set. He inspects two of the stone pawns. One is black, the other is white. 13-year-old Jacob walks up and asks what it is. The Boy in Black says a game. You play it. Jacob asks how he knows, and the Boy in Black shrugs. It's obvious to him. He says he just knows. He'll teach Jacob how to play if he promises not to tell Mother. She'll just take it away. Jacob agrees, and we see that the two boys love each other dearly.
At the cave, Mother works at a loom. And even though the boys are 13 years older, Mother doesn't appear to have aged a day. Jacob comes in, and Mother asks where his brother is. Jacob says down at the beach staring out at the ocean. Mother seems a little concerned about this. Jacob asks if he can help her. Mother briskly points to tangled thread to sort. She asks what they were doing at the beach. Jacob takes a moment, thinks about the promise he made his brother, and simply says they were walking. Mother asks him if he loves her, and Jacob says yes. Then, she says, tell her what happened.
Later, Mother joins the Boy in Black at the beach. And we can tell that he is clearly her favorite. He knows that Jacob told her what he found. Mother is good-natured and says that Jacob doesn't know how to lie. He's not like the Boy in Black. He asks her what he's like, and Mother says he's special. He smiles, clearly having great affection for her. He asks if he can keep the game, and Mother says of course. It's why she left it for him. The boy is surprised. The game came from her? Of course, where else would it come from, Mother asks. The Boy in Black says softly across the sea. Mother tells him there is nowhere else. The island is all there is. The Boy asks where they came from, and Mother says they came from her and she came from her mother. He asks where her mother is, and she says she's dead. The Boy asks what's "dead," and Mother says something he will never have to know about.
Cut to Jacob and the Boy in Black pursuing a boar through the jungle when it's suddenly killed by three men. There are other people on the island! Jacob is shocked, but the Boy in Black's eyes narrow. He confronts Mother about it. She is shocked and asks if the men saw them. The Boy in Black says no, and Jacob asks where they came from. They looked like them. Mother says, very seriously, that the men aren't like them. Those men don't belong there. She and the boys are there for a reason. The Boy in Black demands to know the reason, and Mother struggles with telling them, but she breaks down and tells them to come with her.
She leads them blindfolded through a bamboo field. Mother explains she is taking them to someplace that only she can show them. The Boy in Black asks if she knew about the men, and Mother says yes. She didn't tell the boys because the men are dangerous and she didn't want to frighten them. Jacob asks what makes the men dangerous, and Mother says the same thing that makes all men dangerous. They come, they fight, they destroy, they corrupt. And it always ends the same. The Boy in Black picks up on something and asks where they "come" from. Mother quickly says another part of the island. And she warns the boys to never go looking for them because the men will hurt them. Jacob asks why, and Mother says because they're people and that's what people do. The Boy in Black says they're people, so does that mean they can hurt each other? Mother stops, and we can see the pain in her face. She gently pulls their blindfolds off and says no, she's made it so they can never hurt each other.
The boys look past her and see something amazing. They ask what this place is, and Mother says it's the reason they're here. They are standing at a pristine part of the island, a stream shrouded in darkness from the trees surrounding it. The stream flows into a small opening underground and cascades over a waterfall into a crevice. And from inside the crevice rises a pure white light. The light creates a sense that something exceptional and special lies beneath the waterfall deep in the earth.
Mother holds the boys back from stepping into the water. Jacob seems a little confused, maybe even scared, but his brother is fascinated. Almost hypnotized. He asks what's down there, and Mother tells him, with quiet reverence, light. The warmest, brightest light they have ever seen or felt. And they must make sure no one ever finds it. The Boy in Black says it's beautiful, and Mother says yes, it is. That's why they want it. A little bit of the light is in every man, and they always want more. Jacob is afraid and asks if the men can take it. Mother says no, but they will try. And if they try, they could put it out. If the light goes out here, it goes out everywhere. So Mother has protected this place but she can't protect it forever. The Boy in Black asks then who will, and Mother says it will have to be one of them.
Later, Jacob and his brother are playing senet in the jungle when the Boy in Black sees a woman standing in the distance. It's Claudia! She tells him it's all right, don't be afraid. The Boy in Black abruptly tells Jacob he's going to take a walk on the beach and leaves. He finds Claudia in the jungle and asks why Jacob can't see her. She says because she's dead. Claudia asks him to come with her. She wants to show him where he came from. She leads him through the jungle to a village and explains those people came to the island 13 years ago when their ship wrecked in a storm. The Boy in Black asks what's a ship, and Claudia says it's what they use to go from one place to another. It's how they came across the sea. But the boy says there's nothing across the sea. Claudia says there are many things across the sea. Beautiful things. She says this island is not his true home. He came from across the sea, too, and the boy is shocked. He denies it. It can't be true. That's not what his mother told him. Claudia says that woman is not his mother — she is.
That night the Boy in Black returns to the caves, wakes Jacob and tells him they're leaving and never coming back. The Boy has packed his stuff, and Jacob asks why. The Boy says they're going to the people. Jacob says that they're supposed to stay away from those people. They argue, and the Boy in Black says that Mother lied about everything. She's not even their mother!
Jacob starts punching his brother, beating him, when Mother runs up and stops him. Jacob says his brother is leaving and going to live with the other people. Mother is shocked, but the Boy in Black says he knows the truth. There is another place across the sea. It's where he's from, and he's going to go home. Mother asks who told him that, and he says his real mother — whom she killed! He says they don't belong with her and asks Jacob to come with him. Jacob says no. Mother tells the Boy in Black that no matter what he's been told, he can never leave the island. He says that's not true and one day he'll prove it. But until then? He can leave her. And the Boy in Black walks off into the jungle, melting into the darkness.
On the beach the next morning, Mother sits crying. Jacob asks if it's true she killed their mother, and she says yes. If she had let her live, she would've taken them to her people, and those people are bad. She needed them to stay good. Jacob asks if he's good why she loves the Boy in Black more than him? Mother blinks because she knows it's true. But she consoles him and says she loves them in different ways. She asks if Jacob will stay with her, and Jacob says yes. For a while.
Thirty years later, Jacob works the loom as Mother sits by the fire. She doesn't look any older but the years have taken a toll on her. Jacob asks if she's all right, and Mother says she's just tired.
Cut to a clearing in the jungle where the Man in Black works with some men as they dig a well into the ground and lay stones for the side. He looks up and sees Jacob watching. They wave to each other, and the Man in Black joins Jacob for a game of senet. The Man in Black asks if Mother knows about Jacob's visits, and Jacob says yes, but she never asks about him. The Man in Black says then he's sorry he asked about her. Then he asks why Jacob watches them, and Jacob says he wants to see if Mother is right about them. The Man grins. He says Mother is insane but she was definitely right about these people — they are bad. They're greedy, manipulative, untrustworthy and selfish. Jacob asks why he's with them, and the Man says they're a means to an end. He's leaving. He's found a way off the island. Jacob says that's impossible, there isn't a way off the island.
The Man slides his dagger off his belt and throws it. The dagger switches direction and CLANG! Flings to the side of the well. Sticks to the stones. Jacob is stunned. The Man says there are smart men among the group who are curious how things work. They discovered places all over this island where metal behaves strangely. When they find one of those sites, they dig. And this time they found something. He asks Jacob to come with him. But Jacob shakes his head. He can't leave. It's his home. Upset, the Man in Black says it's not his.
Jacob returns to the caves and tells Mother what he learned — that his brother has finally found a way to leave the island. Mother is taken aback. She goes to the dig site and climbs down into the cavern the Man in Black has made to talk to him. He explains he's spent thirty years looking for the place she took him as a child, the waterfall with the beautiful light. He's walked the island end to end and not once came close to finding it. But then he thought what if he could get to that light from someplace else. Figuring out how to reach it took a very long time. Mother asks if the people from the village saw this, too, and the Man says yes. He uses a wood pry bar to pop out a stone, and behind it a ray of white light shoots out from the hole. In the light, she sees what he was carving. It's the beginnings of the wooden donkey wheel. The Man explains that they are going to open a hole, a bigger one, and attach the wheel to a system that channels the water and light. And when it's done, he'll finally be able to leave the island. Mother asks how he knows, and the Man in Black says he's special. Mother asks him not to do this, not to go, and he says he has to go. He doesn't belong there. She realizes it's time to say good-bye and they hug. Then she says she's sorry. But before he can ask what she's talking about, she throttles him forward, smashing his head into the stone wall and knocking him unconscious.
Mother returns to the caves and wakes Jacob telling him it's time. She leads him through the jungle and bamboo field to the stream. Jacob realizes something happened, and Mother says she had to say good-bye to his brother. They reach the area with the underground opening and waterfall, and Mother says Jacob is going to protect it now. Jacob asks what's down there, and Mother says life, death, rebirth. It's the source. The heart of the island. She asks Jacob to promise one thing — no matter what, he won't ever go down there. He asks if he would die, and Mother says it would be worse than dying. Much worse.
She reaches into her satchel and pulls out a wine bottle and a simple silver chalice. She mutters a prayer then pours some wine into the chalice. She offers the cup to Jacob and tells him to drink. Jacob asks what will happen if he does. Mother says Jacob will accept responsibility to protect this place as long as he can. And then he'll have to find his replacement. Jacob says he doesn't want to protect this place. She wanted it to be his brother, but he's all she has. Mother says it was always supposed to be Jacob. She sees that now and one day he'll see it, too. But until then, he doesn't really have a choice. Jacob takes the cup and drinks. There's no magic, no skyrockets, but maybe something deeper. Because when he looks up and meets Mother's eyes, it is a meeting of equals. Mother says now they are the same.
As dawn breaks, the Man in Black regains consciousness. He's outside the well, and the ladder is on the ground. Immediately he knows something is wrong. He looks in the well and sees that it's been filled in with stones. Then he sees a column of black smoke rising from the direction of his village. He runs towards it and finds the smoldering remains of his camp. It's all been burned to the ground. No more shelters. No more people. It's all gone. He realizes Mother killed everyone in their sleep and burned the place down. He finds the charred senet set amongst the ruins, and anger fills his face.
At the caves, Mother returns to find the place trashed and her loom smashed. In the center is the burned senet set. She kneels down to inspect it — and SCHLLIKKT! Mother looks down and sees the tip of dagger sticking out of her chest. Behind her the Man in Black withdraws the dagger. There's no shock, no pain. Only a weary look as she slumps over. He asks why she wouldn't let him leave, and Mother says because she loves him. He can tell she means it. Then she says thank you and dies. Behind him the Man hears something and turns. Jacob is standing there. He's stunned and asks what he did. Jacob grows angrier and charges his brother, punching him in the face! Again and again and again. Beating him brutally.
Jacob drags the Man in Black through the bamboo field towards the stream. The Man says Jacob can't kill him — Mother made it that way. Jacob says not to worry, he isn't going to kill him. Jacob drags him to the underground opening with the waterfall and pushes him into the stream. The current catches the Man in Black and he is swept over the falls and down into the underground cavern. From below comes a rumbling, and we hear the bone-chilling howl of the monster! It's a feral cry of pain and boiling rage. The rumbling builds and the ground shakes — and like a geyser going off, something blasts out of the crevice! It's black smoke. It billows above and then roils into the jungle. It happens so fast, and Jacob is knocked back.
He staggers out into the jungle a little afraid of his first encounter with the monster. He comes across another stream and washes the blood off his hands. As he looks up, he notices the body of his brother. Jacob looks around and sees that the stream burbles out from an overgrown embankment. He realizes that his brother's body was washed through the mysterious underground river cavern and emerged here. Jacob cradles his dead brother's body, picks it up and carries him back through the jungle to the caves. He places the body in the corner, and then gets the body of his dead mother and lays her beside him. He picks up two stone pawns from the senet game — one black and one white — and puts them in a pouch from around his waist. He places the pouch in his brother's hand — and we realize Jacob's mother and brother, the Man in Black, are the Adam and Eve skeletons.
Jacob gently touches his brother's face and says good-bye.