The route of the Obra Dinn on its final journey.

The story of Return Of The Obra Dinn is divided into ten chapters. The narrative is non-linear and starts in 1807, five years after the Obra Dinn set for its final journey.

In 1802, the Obra Dinn has launched from London with a full crew and some passengers, including four Formosans, It-Beng Sia, Bun-Lan Lim, and guards, Chioh Tan and Hok-Seng Lau. The Formosans travel with two main plot devices: a chest containing a shell.

I: Loose CargoEdit

The Obra Dinn is in Falmouth, taking on cargo under the supervision of the Danish seaman, Lars Linde. The rope carrying the cargo snaps, and the pallet crushes another seaman, Samuel Peters. Unbeknownst to the crew, there is a stowaway hiding inside one of the barrels. The stowaway dies when the barrel falls over and hits the ground.

II: A Bitter ColdEdit

As the Obra Dinn sails by the coast of Portugal, two Indian seamen, Soloman Syed and Renfred Rajub, have contracted a fatal lung disease in the lascar house and eventually succumb to it.

Meanwhile, the midshipmen, Thomas Lanke, Peter Milroy, and Charles Hershtik, assist the ship's butcher, Emil O'Farrell, in slaughtering a cow for its meat.

III: MurderEdit

When the ship passes by the Canary Islands, Edward Nichols, the morally bankrupt Second Mate, slips into the cargo hold. He knocks a guard, Hok-Seng Lau, unconscious and breaks into the room containing the Formosan chest. As Nichols is about to take the shell inside the chest, an Italian passenger, Nunzio Pasqua, wanders into the cargo hold and catches him in the act. His theft thwarted, Nichols kills Pasqua to cover up his crimes and possibly gets topman Li Hong to intentionally mistranslate Lau's words, framing him for the murder.

Some time later, Captain Robert Witterel sentences Lau to death by firing line. The Formosans protest Lau's execution, but to no avail. Meanwhile, Edward Spratt, the ship's artist, draws the execution scene.

After the execution, Nichols forms a mutinous group and abducts the chest and two Formosans, incapacitating any crewman who attempts to intervene. One topman, Timothy Butement, attempts to stop the group, but Nichols quickly shoots him down.

IV: The CallingEdit

Second Mate Nichols leads his band of mutineers on an expedition to the Canary Islands when a group of mermaids attack the lifeboats, starting by spearing topman Hong in the chest. Nichols takes cover on his boat, and nearly everyone dies at the hands of the mermaids, with seamen Patrick O'Hagan getting speared, Aleksei Toporov and Alarcus Nikishin being drowned, and passenger Bun-Lan Lim getting clawed.

In the middle of the fight, passenger Sia uses the spear that has impaled Hong to break free from his bonds, takes a knife from the bottom of the boat, and uses it to stab Samuel Galligan, Nichols's steward. Sia takes the shell and places it inside the chest, creating bright beams that stun the mermaids, but the action burns his arm to the bone and costs him his life.

Nichols, the only survivor, hauls the unconscious mermaids onto the boats. As he approaches the Obra Dinn and hails the ship, passenger Chioh Tan, at this point the only surviving Formosan, shoots Nichols and kills him.

V: Unholy CaptivesEdit

While the captured mermaids are hauled on board, Captain Witterel has seaman Hamadou Diom hold Tan for interrogation. With Huang Li, a Chinese topman, acting as translator, Captain Witterel interrogates Tan about the death of Nichols, the mermaids, the chest, and the dead Formosans. Tan is only able to say that the shell must be protected before a mermaid shoots a spike through him and Diom.

The mermaids, even as they are taken to the lazarette, prove dangerous. One of them slaps Thomas Sefton, the ship's cook, with its tail, and seaman William Wasim, one of the crewmen carrying the mermaid to the lazarette, falls down a flight of stairs, leading to him to break his neck. Fillip Dahl, Captain Witterel's steward, witnesses this and later runs off to attack seaman John Naples, cutting off his leg.

Captain Witterel, surprised that his steward of twenty years would act out, brings Bosun Alfred Klestil and his "Frenchman", Bosun's Mate Charles Miner, with him to interrogate Dahl on his actions. Dahl attempts to warn them that the mermaids are cursed and urges that they should be thrown back into the sea, but he gets hauled into the lazarette for his trouble.

VI: Soldiers of the SeaEdit

The ship circles around because of the escalating number of tragedies afflicting the ship. A storm strikes the ship and topman Huang Li gets struck by lightning. Humanoid creatures mounted on giant crabs board the ship and kill more of the crew, starting by spearing topman Nicholas Botterill, spiking carpenter's mate Marcus Gibbs, and decapitating surgeon's mate James Wallace and topman Jie Zhang. Midshipman Charles Hershtik, one of the crewmen fighting the crab riders, manages to kill one by throwing a lantern at it, but he burns to death along with it. Henry Evans, the ship's surgeon, attempts to remove a spiked butcher O'Farrell from the wall, which unfortunately kills him in the process. Then another crab rider comes below deck and begins attacking. Miner attempts to shoot it, but accidentally shoots ship's steward, Zungi Sathi, who, unbeknownst to everyone, crawled behind a wall after being spiked earlier. Winston Smith, the ship's carpenter, who had received a hand mortar from Klestil earlier, shoots and kills the other crab rider as it is spearing him to death.

VII: The DoomEdit

Surviving the crab rider attack, three crewmen, seamen Alexander Booth, Nathan Peters, and purser Duncan McKay, decide to escape. When seaman Lars Linde asks to join the group, Peters refuses and clubs Linde for supposedly killing his brother Samuel (in chapter I), in spite of Linde and Booth's protests that the death was accidental.

West of Madeira, a Kraken attacks the ship, causing the deaths of sixteen further crewmen, those being Artist Edward Spratt, who was strangled by the Kraken; seaman Abraham Akbar, who was crushed by the Kraken; seaman George Shirley, who was pulled (or shot) out the window and drowned by the Kraken; Gunner Christian Wolff, who was shot with a cannon by the Kraken; Third Mate's steward Roderick Andersen, who was crushed by a loose cannon; Midshipman Peter Milroy, who was caught in an explosion; topman Omid Gul, who fell overboard; topman Maba, who was torn in half by the Kraken; aforementioned seamen Nathan Peters, Alexander Booth, and purser Duncan McKay all fell overboard when the kraken flung their lifeboat into the air; the captain's wife, passenger Abigail Hoscut Witterel, who has stepped out to look for her husband was crushed by falling rigging; helmsman Finley Dalton and topman Wei Lee, who were drowned by the Kraken; and Bosun's mate Charles Miner, who was torn apart by the Kraken. The attack leaves only a skeleton crew.

VIII: BargainEdit

Inside the lazarette, Captain's steward Dahl breaks free from the handcuff. He opens the chest and pulls out the shell from it, but he burns off his arm and dies.

During the Kraken attack, Captain Witterel deduces that the mermaids are responsible, so he enters the lazarette and kills off two of them, in the hopes that they call off the attack. He takes two shells and possibly throws them overboard, but this is not fully confirmed in the narrative. Whether due to the shells or the last remaining mermaid calling off the Kraken, the attack stops none the less, and the storm subsides.

Later, Third Mate Martin Perrott and stewards Paul Moss and Davey James enter the lazarette and come across a third shell in Dahl's hands. Perrott gets spiked before he could assure the mermaid that he has come to set it free. Mortally wounded, he orders the stewards to give the mermaid the shell, throw the beast overboard, and lock the door to the lazarette as they leave. He also asks the mermaid to see the Obra Dinn home.

Even later, Moss finds the ship's surgeon, Henry Evans, attempting to enter the lazarette when the key to it has been disposed of. Aware of the functionality of a pocketwatch called the "Memento Mortem" and assuming that the East India Company will use the watch to investigate the ship should it ever make it back to port, Evans ties his pet monkey to a rope, kills it in the lazarette, and keeps its paw before leaving.

IX: EscapeEdit

Meanwhile, Fourth Mate John Davies helps dying Bosun, Alfred Klestil, to a chair in the gun deck. Davies tells him that his "Frenchman" was torn apart and that the Kraken went away with the storm, thanks to Captain Witterel.

Shortly after Klestil dies of blood loss, Gunner's Mate Olus Wiater expresses doubts of Captain Witterel's trustworthiness. He broaches the subject of mutiny with Davies, planning to take over the ship and sell the "wretched fish" and shells. Thomas Lanke, the only surviving midshipman at this point, overhears the conversation and panics, alerting the crewmen of mutiny. Wiater stabs Lanke in the back for his trouble, but Davies intervenes, reaching for Wiater's gun. During the scuffle, the gun blows off Wiater's face. The dust-up catches the attention of First Mate William Hoscut, who rushes to the dying Lanke's aid; and seaman Henry Brennan, who clubs Davies for supposedly killing Wiater with malice aforethought.

Now to the north of Madeira, Evans, James, Moss, and passengers Emily Jackson and Jane Bird attempt to leave the ship, but Leonid Volkov, a Russian topman, catches the group and attacks, getting into a sword fight with Moss. Despite the intervention of Captain Witterel, First Mate William Hoscut, seaman Henry Brennan, and topman Lewis Walker, Volkov stabs Moss, killing him. He proceeds to try to attack the others, but Jackson quickly shoots him down, killing him.

X: The EndEdit

After an indeterminate amount of time has passed, First Mate Hoscut, seaman Brennan, and topman Walker all turn on Captain Witterel and attempt to extort the shells, but he says he has thrown them overboard. The crewmen do not buy the explanation and attack him. The Captain is forced to kill them all in self-defense. He shoots Hoscut with a gun, slits Brennan's throat, and clubs Walker in the head (who has already stabbed his knife into the captain's right side).

Overcome with grief, Captain Witterel sits beside his wife's body, laments the death of Hoscut, and asks for her forgiveness before shooting himself.

Back in FalmouthEdit

Five years later in 1807, the Obra Dinn drifts back to port at Falmouth. An East India Company insurance inspector is summoned to determine what happened aboard the ship. They are given a catalogue and the pocketwatch, both of which surgeon Henry Evans mailed to the East India Company from Morocco.

The inspector completes their investigation and leaves the ship as the weather is about to get bad. After they leave, the Obra Dinn sinks in the storm. The inspector then prepares a full insurance assessment and mails the book back to Henry Evans.

London a year laterEdit

Roughly a year later, Henry Evans dies in Africa due to an illness, and one of the surviving passengers, Jane Bird sends the inspector a letter about how Evans felt about the inspector's performance. If enough fates were confirmed, Bird sends the catalogue back to the inspector. The inspector gets a chance to find out what happened to crew members in the lazarette of the Obra Dinn as the package also contains the paw of a monkey that died in the lazarette. The story ends as the inspector places the fully completed catalogue in their bookshelf.

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