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 sail. This article lists events in an in-universe chronological order.
In 1802, the Obra Dinn launches 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.
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 also dies when the barrel hits the deck.
When the ship passes by the Canary Islands, Second Mate Edward Nichols 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. It is implied that Nichols gets topman Li Hong to intentionally mistranslate Lau's description of the incident as a confession, 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 organizes several seamen to help him steal the chest and abduct two of the Formosans. In the course of this escape, they attack several other crewmen. One topman, Timothy Butement, is shot dead as he attempts to stop the group.
Second Mate Nichols' band begins rowing their two boats towards the Canary Islands, but a group of mermaids attack the lifeboats, starting by spearing topman Li 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 her face clawed.
In the middle of the fight, passenger It-Beng 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' steward. Sia then 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.
The captured mermaids and the corpses of Nichols, Lim, and Sia 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 one of the captured mermaids shoots a spike through him and Diom.
The mermaids, even as they are hauled down 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, breaking his neck. After the mermaids are secure in the lazarette, seaman John Naples is possibly tasked with guarding the door. Fillip Dahl, Captain Witterel's steward, is upset that the mermaids are being held and attempts to free them, and attacks Naples, cutting off his leg and resulting in his death.
Captain Witterel, surprised that his steward of twenty years would do such a terrible thing, brings Bosun Alfred Klestil and his "Frenchman", Bosun's Mate Charles Miner, with him to interrogate Dahl. 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 and shackled to the floor for his trouble.
After these events, the ship turns around and heads back to England. Shortly after the ship comes about, however, a storm strikes. Topman Huang Li gets struck by lightning while working in the rigging. At the same time, mysterious humanoid creatures mounted on giant crabs board the ship. They attack and kill more of the crew while making their way to the belly of the ship – whether their agenda is to capture the shells or the mermaids is unclear. They spear topman Nicholas Botterill on the main deck, spike carpenter's mate Marcus Gibbs, decapitate surgeon's mate James Wallace and topman Jie Zhang on the Orlop Deck. 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. The second crab rider is close behind. 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. The crew pursues the crab rider to the cargo deck, and Winston Smith, the ship's carpenter, shoots and kills the other crab rider with a blunderbuss as it is spearing him to death.
Surviving the crab rider attack, three crewmen, seamen Alexander Booth, Nathan Peters, and purser Duncan McKay, decide to escape in one of the boats. When seaman Lars Linde asks to join the group, Peters refuses and clubs Linde for 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. Meanwhile those of the crew that had escaped in a lifeboat – seamen Nathan Peters, Alexander Booth, and purser Duncan McKay – all fell overboard and drowned when the kraken flung their lifeboat into the air; the captain's wife, passenger Abigail Hoscut Witterel, who stepped out to look for her husband, was crushed by falling rigging; helmsman Finley Dalton and topman Wei Lee were pulled into the sea and drowned; and Bosun's mate Charles Miner was torn apart. The survivors after the attack make only a skeleton crew.
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 finding it full of unknown substance that resembles mercury.
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, and the storm subsides.
Later, Third Mate Martin Perrott and stewards Paul Moss and Davey James enter the lazarette and come across the 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.
Now north of Madeira, Fourth Mate John Davies helps the 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 gives chase and stabs Lanke in the back for his trouble.
Meanwhile on the main deck, Evans, James, Moss, and passengers Emily Jackson and Jane Bird attempt to leave the ship on the last remaining boat, 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.
Unaware of the shot fired on the main deck, Davies attempts to stop Wiater from further harming the mortally wounded Lanke, reaching for Wiater's gun. During the scuffle, the gun blows off Wiater's face. The dust-up catches the attention of First Mate Hoscut, who rushes to the dying Lanke's aid; and seaman Brennan, who clubs Davies, wrongly believing that Davies killed Wiater on purpose.
As Horscut tends to the dying Lanke, Lewis Walker throws Volkov's body overboard. The boat carrying Jackson, Bird, James, and Evans is gone, and Captain Witterel slumps over, utterly defeated.
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 Falmouth
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 and are given a catalogue and the pocketwatch, both of which surgeon Henry Evans mailed to the East India Company from Morocco.
The inspector completes the investigation and leaves the ship as the weather is about to get bad. After leaving, the Obra Dinn sinks in the storm. The inspector then prepares a full insurance assessment for the East India Company and mails the book back to Henry Evans.
London a year later
Roughly a year later, surgeon 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 the bookshelf.