- A Private Detective, Edward Pierce is a mission to find the truth behind the death of an acclaimed artist and her family on a Darkwater Island in Boston.
- October, 1924. Edward Pierce is a Great War veteran turned private detective working in Boston. He has become reliant on alcohol and sleeping pills to suppress his nightmares of the conflict, yet recently he's experiencing nightmares of a different kind, regarding some otherworldly voice talking to him and a scene of a ritual. One day, a respected figure enters his office asking for his services, the figure is Stephen Webster, industrialist and art collector. Some months ago his daughter and her family died in a fire at their home, his daughter is Sarah Hawkins, a painter, known for her vivid and macabre style. She lived on an island called Darkwater, the police reports state that the fire was an accident, however, Sarah had mental problems and reported hallucinations and it's theorized she may have started the fire. Webster is doubtful his daughter would commit an act and asks Pierce to investigate further. All he has to aid the investigation are the police files and a portrait sent to him shortly after Sarah's death. Pierce examines the portrait, it is of Sarah and her son, Simon being menaced by a silhouette bearing an occult symbol on its chest, Pierce agrees to investigate, he traces the island to the coast of Boston.
Upon arrival Pierce learns about the culture and people, the island used to be a successful whaling community until a disappearance of whales lead to a famine in 1847. One such ship, the Scylla, ventured out to sea and captured a massive creature that saved the island. Pierce meets the prominent locals, Roy Mitchell, a bartender, Captain James Fitzroy, the harbormaster, Catherine Baker, gang boss and bootlegger and Officer Ethan Bradley, the last of which is overseeing a mutilated Orca that has washed up. Fitzroy provides Pierce with manifests that were written by Sarah's husband, Charles Hawkins, mostly incomplete, with a nearby address, Warehouse 36. Pierce infiltrates the warehouse and finds proof of someone's presence along with a peculiar portrait. Bradley walks in and finds Pierce snooping, the latter directs Bradley's attention to the portrait, Bradley was on the Hawkins case and he recognizes the portrait, it's been taken from the Hawkins mansion and drives Pierce there.
Pierce finds the graves of the family, Charles' grave has been vandalized, Bradley is confused as the family caretaker, Silas Winchester, wouldn't have allowed such a thing. Pierce tries the mansion backdoor, only for Silas to jump him, he still guards the grounds out of respect to his employers, Pierce is able to retrieve a key from Silas and he enters the building. Pierce starts his investigation in the dining room, there is evidence of an argument and a peculiar meat served up. In the living room was where the fire started, an oil lamp was the cause, Pierce finds blood on the shards confirming the couple argued which lead to violence. Further in Pierce searches the family rooms, it seems Sarah and Simon were on sleeping pills and both were having visions of some horrific monster. A noise from the attic draws Pierce's attention, he finds a portrait of himself and is jumped by a masked figure, Pierce chases them downstairs into Charles' study, a secret door is found hidden behind a bookcase. It leads underground to a cave under the island where more masked figures are conducting a ritual. Pierce is attacked and falls down into a pit from his nightmares, the bodies of sea life are scattered as offerings for rituals, Pierce ventures forth to witness another ritual with Bradley, the latter draws his gun on the cultists, the leader pulls back his hood to reveal Charles Hawkins, alive but burned and with Cephalopoda mutations. Bradley fires on him to no avail and is impaled on Charles' tentacles, Pierce runs as a cave in occurs, he almost makes it out but is caught under rocks.
Pierce gains consciousness in a hospital asylum, where Doctor Thomas Fuller experiments on him, during his bouts of awareness Pierce sees Bradley alive. Pierce awakens in a cell and witnesses the guards bundle a patient named Francis Sanders out of his cell, soon after, Marie Colden, a doctor at the hospital, releases him from his cell, she tells Pierce to leave while he can as Fuller is experimenting on all the psychiatric patients. Pierce creates a distraction to draw guards away from the exit and he meets Francis, he was admitted after a hysterical attack that made him blind himself. He knew Sarah Hawkins and purchased a painting from her "The Shambler". Which made Francis gouge out his eyes and he's afraid to leave the asylum for fear something will get him, as it happens some supernatural force murders him in front of Pierce, the latter hurries out of the room and inhales sleeping gas being dispersed, he passes out again with Bradley standing over him.
Pierce has another nightmare of a gargantuan marine life and awakens in the Hawkins mansion, Bradley and Colden are there, Pierce addresses Bradley's death to which the latter has no memory of, or prior to the underground cavern. Pierce also mentions meeting Sanders, yet the details of his death are unbelievable. Colden mentions Sanders was an art collector and Pierce should meet his widow, Irene. Pierce arrives at the Sanders estate, Irene has been informed of her husband's demise, Baker is there on business, she leaves Irene to speak with Pierce. Irene admits some resentment to Sarah Hawkins because of the time Francis spent discussing her work, even more so after his last purchase drove him mad. Pierce heads to the mansion's art gallery to examine the painting, he finds a document stating that Sarah refused to sell the painting for quite some time only to give to Francis for free. In the gallery Pierce studies the portrait, it's of some hideous monster which comes alive, Pierce banishes it back into the portrait by stabbing the canvas with a ritualistic dagger. The dagger was bought from an antiquarian, Algernon Drake, he runs a bookstore, The Nameless Bookstore, Pierce travels there.
Pierce finds the bookstore has been broken into, with his investigatory skills he determines that Charles was the thief, he attempted to break into a safe in the back room but an occult ward blocked him. Pierce unlocks the safe and finds the Necronomicon (Book of the Dead), the book sends Pierce into an out-of-body experience which enables him to see through the eyes of others, he's living Colden's experiences at the hospital, she's examining a patient that is mutating, which Colden believes is caused by Fuller's experimentation, she sneaks into his office and finds a wax cylinder of Fuller's consultation of Sarah Hawkins. Fuller also had encounters with Charles and James Fitzroy and Sarah was the connection between them. Colden heads to the basement where Fuller conducts his experiments only for Fuller to tranquilize her. Pierce awakens from his trance and finds Drake pointing a gun at him, believing him the thief. Pierce explains his experience with book and realizes he must save Colden.
Pierce enters Fuller's office through the window, inside is a framed photograph of Fuller dated 1849, which brings into question Fuller's age. Pierce's search is hindered by more hallucinations of the Shambler and the abyssal voice from his nightmares. He finds Colden dead, Fuller experimenting on her. Pierce attacks Fuller but Colden reanimates briefly to knock him out. Pierce awakens and progresses further and finds Sarah, alive in a cell. She is hiding from something trying to call her, they escape and encounter Charles again, he attacks Pierce and claims he hid Sarah to hid her from a cult who perceive as an Oracle. Sarah impales Charles through the throat with a poker and the two head to the mansion.
Back at the mansion Drake asks Pierce to find an amulet to protect Sarah from supernatural influence. Pierce finds it, however the police arrive and arrest Pierce for numerous charges since his arrival. The voice greets Pierce again in his cell, followed by a hallucination of the cells flooding and the voice appearing as a human silhouette before Pierce. It introduces itself as Leviathan, offering knowledge beyond human comprehension. Pierce has another trance seeing Sarah's whereabouts, she and Drake are about to conduct a ritual that will banish the Shambler for good. The ritual is performed and the Shambler is banished, although Drake could die here if the player doesn't stop the Shambler from dragging him into the portrait with it. The ritual has drained Sarah of her strength and she can no longer ignore the call from beyond.
Pierce has witnessed this turn of events from his cell, Chief Henry West approaches Pierce again with more questions which are interrupted by a report of a disturbance, Pierce sees this as the beginning of something terrible but his warnings are ignored. Leviathan meets with him again and shows him more visions of the people of he's met on Darkwater. Visions of Baker shooting Pierce, Bradley suffering from nightmares and Sarah painting his portrait. Pierce has another trance, this time of Baker, Chief West has been killed by the local fishermen and his body was dumped in one of her warehouses. Baker investigates the crime scene, she finds a cultist dagger and a pack of smokes belonging to Fitzroy. Her investigation is interrupted by gunfire, the fisherman are under Leviathan's possession and are attacking everybody.
Bradley releases Pierce from his cell and hands him a gun, he's succumbing to Leviathan's control, Pierce can choose to shoot Bradley or spare him. Outside Pierce is forced to kill attacking locals and finds both Baker and Mitchell wounded and is tasked with bringing a first-aid kit to either one, whomever is saved grants Pierce a key to the whaling station.
In the whaling station Pierce finds Leviathan floating in the dock, it seems the Leviathan was the legendary catch of 1847 that saved Darkwater from famine, and it wished to be caught so that the islanders could feast on its flesh and possess them. Its flesh also granted immortality, Fuller, Charles and Fitzroy were the ones who caught Leviathan. Pierce is put through a series of hallucinatory ordeals to test his devotion, Pierce does them regardless of whether the player accepts of refuses, if the latter, Pierce will merely make a feeble attempt to resist, these ordeals are taking a sleeping medication, eating Leviathan's flesh and shooting Fuller. These ordeals lead to the destruction of the whaling station and Leviathan's escape, Pierce falls into the water where Leviathan speaks to him one last time before returning to the depths.
Pierce washes up on the coastal island of Alabaster Point, he encounters more hallucinations, against Colden, Fuller, Charles and Sarah, all of which goad him to fulfilling his destiny, to release an ancient god. At the very terminus of the island Pierce finds Sarah with Fitzroy and Drake being held hostage (If saved). Sarah has now embraced the cult's ideals and Pierce is the one to release the god.
Four possible endings can happen here depending on Pierce's sanity.
Perform the Ritual: Pierce accepts to perform the ritual and summon the ancient god, Cthulhu, which drives all onlookers mad and kill each other.
Counter-Ritual: Drake must be present. Drake traps Cthulhu within Pierce, who is permanently maddened and held in Darkwater asylum.
Sacrifice: Pierce's sanity must be low. Pierce loses his mind and shoots himself. Later his office is being cleared out and a portrait of him shooting himself is displayed in the room.
Refuse: Pierce's sanity must be high. Pierce is stable enough to refuse to perform the ritual, Sarah realizes that no-one can make him do it and that all she sacrificed was in vain, including her son. She throws herself off the cliffs in despair. Pierce returns to Boston, traumatized and drinking in his office, staring at the portrait of Sarah's corpse.
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