After Blackthorn commands them to "Kill the savage first," Nathan and Tuffley fire at Crusoe and Friday, who are eagerly running toward them. Crusoe is in disbelief as a bullet narrowly misses them. Friday fires back and hits one of the sailors. Crusoe can't process what's happening as bullets zing past them and kick up sand. Friday grabs Crusoe and pulls him into the jungle. On the beach, the Captain tells Blackthorn he didn't realize it was a murder mission. He asks him how he could do that to Crusoe, who loves him. Blackthorn shouts that he doesn't pay the Captain to ask him stupid questions.
In the jungle, Nathan and Tuffley hunt Crusoe and Friday. Within earshot of them, they muse that Crusoe must have become uncivilized, to keep company with a savage. They agree that killing him will be an act of mercy. After they move on, Crusoe explains to Friday who the two are. Tuffley returns to the beach and sends more men to continue the search. Despite what just happened, Crusoe shocks Friday when he says they can't leave without Blackthorn. He wonders if Tuffley and Nathan have already killed him.
Crusoe sneaks up to the landing camp on the beach and overhears Blackthorn, Nathan and Tuffley talking. Tuffley tells Nathan that Blackthorn hired an assassin to kill Crusoe on the boat from London. Crusoe is crushed at his words. Blackthorn tells Nathan to let the men hunt the two down while they go to the treehouse to retrieve something that Crusoe left behind. Crusoe knows he means his Bible with his family records. Nathan is disappointed that they'll miss the kill. Blackthorn says he'll be happy just to view Crusoe's remains.
In the jungle, two sailors ambush Friday and whack him over the head. He's momentarily stunned until Crusoe arrives, fueled with rage, and flattens the two with his fists. He apologizes to Friday and tells him what he overheard. Meanwhile, Tuffley, Blackthorn and Nathan cross the sulfuric lake via a ladder, which Blackthorn throws into the lake once they're across. Crusoe tells Friday he honestly thought Blackthorn loved him and feels bereaved. Friday says they'll kill him. Crusoe says yes, once he knows what this all means for Susannah and their children.
In England, Olivia and Susannah search Blackthorn's house for her children. Meanwhile, at an orphanage, Daniel and Sophie Crusoe sit at a table with a bunch of other bedraggled children. A terrifying monk instructs them that they will make fine leather accessories for ladies and gentlemen. If they damage or cut themselves and bleed on the hide, they'll be punished. Same for talking. Daniel cuts himself but Sophie quickly changes hides with him and takes the blame. For punishment, the monk locks her in a dark room.
Blackthorn, Nathan and Tuffley come to Blackthorn Falls, but Blackthorn doesn't divulge that Crusoe named them after him. Meanwhile, Crusoe and Friday pole vault over the broken bridge. When Friday finds Tuffley's discarded handkerchief, they realize that the three are way ahead of them. Blackthorn, Nathan and Tuffley cross the ravine via the rope and are greeted by Dundee. Nathan throws a rock at him and misses, scaring him away. Tuffley starts to sever the bottom rope to stop Crusoe, until Blackthorn asks how he expects them to get back. Tuffley stops halfway through as Blackthorn glares at him.
On the cliffs, Crusoe wonders what Blackthorn wants with his Bible. The same for Tuffley, who asks Blackthorn himself. Blackthorn hedges, but Tuffley persists. Blackthorn says he wants the one piece of paper that could take away his entire fortune. That paper is the certificate that Gallerne told Susannah about which identifies Crusoe as Blackthorn's brother's legal heir. Crusoe and Friday come to the canyon crossing. Crusoe steps on the rope and starts to cross. It snaps and Friday pulls Crusoe to safety. Friday says there's another way, remembering the Spanish Guard built a raft to cross the river.
The three come upon Crusoe's treehouse. Nathan and Tuffley are appalled and compare it to living like an ape. Blackthorn, who had marveled at it, doesn't comment. In the treehouse, Blackthorn empties out the contents of the Bible as the other two trash the place just for fun. Blackthorn fanatically goes through each piece of paper, looking for the certificate. As Friday and Crusoe raft across the river, Blackthorn, coming up empty, hurls the Bible into the jungle. Furious, he commands them to burn everything. Tuffley and Nathan need no prodding to comply.
As Crusoe and Friday race toward the treehouse, Blackthorn, with a gleeful Tuffley and Nathan, set it ablaze. Crusoe and Friday arrive just in time to see their home fully engulfed in flames and watch in horror. In the morning, as they go through the smoldering ruins of the treehouse, Crusoe finds his Bible, safe because Blackthorn threw it, but its spine is broken and reveals a folded paper inside. Crusoe takes it out, reads it. Shock registers on his face as learns the truth about his father. Everything is falling into place.
Friday tells Crusoe they know the island and will pick them off, one by one. Crusoe, still dazed, regains his composure when Friday hands him his undamaged sword that he recovered from the fire. Meanwhile, Blackthorn, Tuffley and Nathan come to the crossing to see the unusable rope walk. They go to the river bed where they find the raft. Since it's too small to hold all three, Blackthorn crosses first, as Crusoe and Friday watch. Wanting to split them up, Friday scares off Tuffley and Nathan by firing arrows at them once Blackthorn is on shore on the other side.
As Friday pulls the raft back across the river, Crusoe emerges from the jungle and tells Blackthorn he has what he's looking for. He holds up the piece of paper and instructs Blackthorn to go back to his ship where he'll meet him. Blackthorn threatens to just sail off, but Crusoe taunts him with the paper and knows he won't. Blackthorn leaves, and Crusoe has Friday secretly follow him to make sure he safely gets to the ship. Friday asks if he wants Blackthorn to have an "accident." Crusoe says, "No, I want to be able to look into his eyes," then leaves to deal with Tuffley and Nathan.
On the ship, the Captain, with carpenter in tow, warns the pilot, who has locked himself in his quarters for days because of what everyone thinks is drunkenness, to come out or be flogged sober. They hear him groan from inside but he's not opening it. They break down the door and smell a foul odor which forces them to cover their mouths and noses. Both are horrified when they see the pilot isn't drunk, but covered with Black Pox. The Captain orders the carpenter to replace the door and tell no one what they saw. Meanwhile, Friday follows Blackthorn, whose resolve is waning.
Tuffley and Nathan reach a dead end on the beach and need to turn back. Crusoe surprises them from behind and says they'll have to get through him first. Tuffley rises to Crusoe's challenge, sneering that he's seen how he is with a sword. Even so, he tells Nathan to jump in if Crusoe's any good. Tuffley goads Crusoe with news about Susannah being in a madhouse and his kids in an orphanage. Nathan taunts him for being so gullible. Tuffley raises his sword, confident this is going to be easy.
Crusoe goes at Tuffley, who quickly sees that Crusoe isn't the novice he once was. As Crusoe launches a vicious onslaught, Tuffley's smirk fades and he abandons his classical style to fight for his life. Crusoe quips that he's only had cannibals and pirates to practice with. Tuffley calls for Nathan to join in. Now it's two on one, but Crusoe fends them off and gets some well-deserved punches in before he slices Tuffley's sword arm. Tuffley drops his sword as Crusoe runs his sword through a disbelieving Nathan. Nathan dies in a heap and Crusoe holds his sword to Tuffley's throat. He says, "You can share what you know or take it to your grave."
As Crusoe carries Nathan's body through the jungle, Tuffley, holding his injured arm, divulges everything about Crusoe's family and the Blackthorns. They reach the river, where Crusoe tosses Nathan's body in. Tuffley watches in disgust as the piranha swim toward it and start to devour it. With the fish busy consuming a large meal, Crusoe warns Tuffley to keep his slashed arm out of the water as they wade across. Meanwhile, the sailors ambush Blackthorn, thinking he's Crusoe. Blackthorn yells at them, but says Friday's behind him and to catch him the same way. "Take him alive," he commands.
After crossing the sulfuric lake, Tuffley wonders why Crusoe doesn't just kill him. Though it would give him pleasure, Crusoe says he never killed a man who didn't force his hand. Crusoe asks if Blackthorn had his mother drowned. Tuffley says Blackthorn won't say. Crusoe asks Tuffley why they're enemies. Tuffley doesn't know, but suggests money and position. When asked, Tuffley confirms he'd stab Crusoe in the back at first chance. It's the nature of the beast. On the ship, the Captain spots Tuffley and "Bosun" rowing toward them. But really, it's Crusoe in Bosun's hat. On the beach, Bosun, missing hat and coat, and his men lie unconscious or dead.
They board the ship and Crusoe reveals himself. Crusoe offers Blackthorn the certificate in exchange for safe passage to England. He asks if Tuffley's tale about his family is true. Blackthorn says they aren't happy, but unharmed. Crusoe wants his solemn word that no further harm will come to them. Blackthorn reminds him he broke an oath he took on a Bible. Crusoe blindsides Blackthorn by asking him to swear on the soul of the woman he loved and lost, his mother Alice. Crusoe asks if he had her drowned. Blackthorn softly says, "No." Then, he swears on her memory.
Crusoe tears up the certificate. Blackthorn says he just tore up a fortune, but Crusoe says going home is worth that much to him. Blackthorn promises to keep his word, but adds that he said nothing about Friday, who two sailors pull up deck. They drag the bound Friday and perch him precariously on the ship's rail. Blackthorn tells Crusoe he can choose to save Friday or watch him drown as they sail away. Crusoe grabs a sailor's sword and fights his way to Friday. He puts his sword to the Captain's throat and stops, seeing his eyes are bloody. He pushes Friday overboard and jumps after him.
In England, accompanied by Olivia, Susannah buys her children, the heirs to the Blackthorn fortune, back from the orphanage with Blackthorn's priceless ancient necklace. On the island, Crusoe tells Friday why he pushed him overboard. He saw blood in the whites of the Captain's eyes, which is the first sign of Black Pox. He says that no one on that ship will reach England alive. As Friday, Crusoe and Dundee watch the doomed ship sail away, Crusoe says he has faith that one day God will make the purpose of his struggles clear to him. "And next time, we're taking the dog," he says.
On the ship, Blackthorn goes below deck and hears groaning. He turns toward the sound and sees the door to the pilot's room which has been sealed with wax. He's curious at the smell of vinegar on the door and touches it. The door pops open and the stench rushes at Blackthorn, who covers his face. He asks who's there, and the pox-ravaged Pilot stumbles toward him as if he's karma, impersonated. Blackthorn, knowing it's the highly contagious Black Pox, backs away in sheer horror and runs up the stairs.