Crusoe wakes to see Susannah. He thinks he's dreaming, but she says he's not. He stands and kisses her, disbelieving and ecstatic at the same time. They walk to the beach, but her ship isn't there. Susannah figures the captain sailed off to avoid the dangerous currents. Crusoe takes her to the treehouse where Dundee only greets him. Crusoe calls for Friday and gets a chest pain. When they get up to the treehouse, they see it's been ransacked and is covered with ash. He remembers smoke and falling. Susannah asks him about a gash on the back of his head.
Crusoe asks Susannah how she saw a fire when there wasn't one. She says there must have been. Crusoe wonders if they are dead. Susannah says they aren't dead yet, and asks him the last thing he remembers before losing consciousness. He remembers making a flag with the ensign of his ship to take to the south cliffs. Friday had been finishing his distinctive spear, which he hadn't taken with them. However, now it's gone so he's been here since. Crusoe calls for Friday, coughs. Susannah coughs too, but says she's just getting over sea sickness. Crusoe is frustrated that he can't remember what happened.
Crusoe examines Susannah's wishbone necklace. She assures him that he'll remember, and says to trust her. They leave for the south cliffs and miss seeing Friday's new spear, snapped with a bloody handprint on the shaft. As they walk, Crusoe has trouble breathing, then remembers that he and Friday hid where they are now standing. On the way back, Friday had a small dead deer he'd found. Crusoe remembers they were being stalked by something, and he thought the deer was attracting it. Friday brought the deer to the treehouse, which is when the smoke started.
Susannah tells Crusoe not to worry about Friday, whom she thinks went hunting. They reach the south cliffs but again, Susannah's ship isn't there. Crusoe notices that Susannah has a fever. He looks at her necklace again, and remembers where he saw it. He and Friday were hoisting the flag, and he saw a wishbone-shaped arch on the beach. When they investigate it, they see it's made from a boat from Crusoe's ship, the Triton. He and Friday see several graves and a skeleton. They find a cave, which has an "N" on the wall, the mark of Captain Neugent.
Figuring the skeleton is Neugent's, Crusoe wants to bury him. In the cave, they find barrels of gunpowder that Neugent used to mine quartz. Why he would want to do that escapes them. Friday finds a leopard claw and the deer. He worries the cat will return, but Crusoe, set on burying Neugent, starts digging. Back with Susannah, Crusoe is sad that Neugent buried his colleagues and died alone. All only a day away from him. Crusoe wonders if a leopard was tracking them and wants to go back to find Friday. Susannah doesn't want to delay the ship sailing, which may risk the crew's lives.
Susannah tells Crusoe that he doesn't know for sure that Friday's hurt, then tries to help him remember more by focusing on the deer. He remembers taking the deer to the tree house and seeing an "N" branded on its side. A bundle of burning grass is thrown into the treehouse, filling it with smoke. They slide down their ropes, but on the way down Crusoe is beaned in the head with a quartz rock. He falls, sees Friday land, grab his spear, only to have it shot in two by Neugent, who then pistol whips him into unconsciousness.
Back with Susannah, Crusoe realizes that Neugent is alive. Worried about Friday, he wants to get back to the treehouse but Susannah says he's probably not there. Crusoe figures he's probably taken Friday to his cave. In the cave, Friday kneels, chained, beaten and frightened. Neugent says Crusoe has nothing compared to him and his diamonds. Friday stands and says they are quartz, not diamonds. Neugent beats him into submission. As they near the cave, Susannah coughs and falls. She puts her hand on his chest, leaves a bloody handprint which he bandages. She fights a growing drowsiness.
Crusoe walks her down to Neugent's beach. She coughs up blood, which Crusoe sees, horrified. She asks him to recite the prayer she said for the man he and Friday buried at the beach, and he does. As he finishes, he realizes they buried the man in the flag and never flew it. He looks at the bare flagpole and asks Susannah how she saw a flag they never flew. She tells him to find Friday, who can save him. And, to survive, "For us." Susannah dies, but before he can react, he's out of the daydream, alone, weak, in pain and coughing up blood.
Crusoe is nudged awake by Friday, who is chopping at rock with an axe chained to his arm. He tells Crusoe not to move, as Neugent is nearby and watching. He gives the delusional Crusoe medicine that Neugent gave to him to reverse the poisoning effects of the smoke bomb. He says Neugent is crazy and wants Friday to build him a palace. Thinking he's a king, he makes Friday call him "My Liege." Neugent orders Friday to keep chopping and makes him kneel. Friday asks for more medicine to be able to breathe. Neugent says he'll breathe when he says he can breathe.
Neugent marches Friday back into the cave and makes him kneel as he shows him the plans for his palace that he says will be built from Friday's blood and sweat, and decorated with jewels. He points to a place where he'll display Crusoe's skull, once the vultures have picked it clean. Back to work under Neugent's gaze, Friday feigns coughing. Neugent gives him medicine, which he sneaks to Crusoe. Neugent walks toward Crusoe's hiding place, and Friday feigns another coughing fit and collapses to divert him. Neugent responds by smacking him hard.
When Neugent leaves the cave, Crusoe sneaks in to try and free the shackled Friday. Crusoe hasn't brought any weapons with him and fumbles around the cave looking for something to pick the lock. Friday says Susannah was a hallucination that Crusoe made to lead him to the cave. Crusoe hears his name from behind. Neugent has come back and has his pistol on Crusoe. He chains Crusoe and makes him kneel with Friday. He holds out a Bible and makes him swear to tell the truth. Seeing it's the Bible his father gave him for the voyage, Crusoe is angered but quickly reels it in when threatened.
Neugent holds "court," accusing Crusoe with theft of land and property, mutiny, and a host of other charges. He finds him guilty and sentences him to hang. At dawn, Friday rigs the noose under Neugent's unsure direction. Crusoe laughs at him, shaking Neugent's confidence. He tells Crusoe he knows what he's doing. Crusoe suggests letting him stand to measure him more accurately. He does, and Crusoe snatches his measuring device and smashes it. Friday swings down from the makeshift gallows, knocking Neugent unconscious. He moves to shoot Neugent, but Crusoe stops him. They break each other's chains and tie up Neugent.
Crusoe and Friday push a tied-up Neugent along the shore, back toward the treehouse. Friday doesn't understand why Crusoe is sparing his life. Crusoe says desperation can make a man forget himself. Friday grabs Neugent's cat 'o' nine tails which he's used liberally on Friday, and tosses them away. Neugent curses him for stripping him of his symbol of power. Crusoe realizes he forgot his Bible and runs back to get it. Outside the forest, Neugent feigns fainting, distracting Friday enough to attack. They grapple, Neugent knocks Friday out and runs back toward the cave.
Inside the cave, Crusoe looks for his Bible. Neugent throws in a smoke bomb but Crusoe kicks it back toward him before he breathes too much in. Crusoe tries to talk to him, but is answered with a gunshot from Nugent's pistol. It misses and they fight, knocking the supports loose which causes the cave ceiling to become unstable. As it starts to crumble around them, a discarded torch ignites a sailcloth. The flames move toward the barrels of gunpowder.
Friday arrives to see the cave entrance blocked by boulders and heaves them away from the entrance. Once he clears enough, he calls for Crusoe to get out. Crusoe tries to convince Neugent to leave the cave but the he runs after his precious cat 'o' nine tails and rants at Crusoe that he's king of the island who has sentenced Crusoe to death. Crusoe, unable to sway the madman, runs for the entrance. As Friday and Crusoe race to reach maximum distance, the cave explodes behind them.
Crusoe breathed in enough of the smoke bomb to see Susannah again. Now, she's healthy. Friday tells him that she isn't there, but Crusoe goes to her anyway. He tells her he thought she was dying. She's stronger than he thought, she says. She has to leave, but Crusoe says he'd choose madness if it meant he could stay with her. As Friday insists he take the medicine, she tells him to stay strong. He drinks the medicine, and Susannah is gone.
As Crusoe carves a gravestone for Captain Neugent, he tells Friday it's his son's birthday today. A son whom he's not sure is even alive. Friday says he can't choose what's happening where he can't see, but can choose what he believes. Crusoe envisions them having a party. Everyone there; his father, Susannah and Sophie in new dresses and Blackthorn who is hosting the party. Thousands of miles away in London, Susannah, Daniel and Sophie tend to James Crusoe's gravestone. Sophie asks if her father is dead. Susannah says no, and tells Daniel that wherever he is, he knows it's your birthday and is thinking of you.