The Sinking City is a bit of a mess to play, but it tells a pretty intriguing Lovecraftian story. If you wanna know what happens, but don't feel like investigating the buildings of Oakmont, then let us tell you the spooky tale of The Sinking City.
Welcome To Oakmont
Charles Reed is a former Navy officer and war veteran, who now works as a private eye in Boston. For some reason, an incident during the war has granted him strange psychic powers, as well as horrific visions and nightmares. When an invitation arrives with an offer to help him get rid of these hallucinations, he jumps on a boat to the mysterious island of Oakmont.
When he arrives in the city, it's in pretty rough shape. It has been decimated by a brutal flood, and dead fish and other sea life are scattered all over, along with some monsters that the locals seem to just kind of accept as if they were commonplace.
He meets two important people right off the bat: Johannes van der Berg, a yellow-suited man who sent the invitation, and Robert Throgmorton, a very wealthy and powerful scholar who also happens to look exactly like a very intelligent ape. Johannes leaves Reed to attend to other matters, while Throgmorton hires Reed to find out what happened to a research expedition he funded, as well as the whereabouts of his son who was also on the expedition.
Unfortunately, after some sleuthing, Reed finds Throgmorton's son Albert dead in the basement of a nearby building. He was killed by an Innsmouther, who are people that have strange fish-like features. Throgmorton is heartbroken. However, he knows something sinister is happening in Oakmont, and he hires Reed to discover the root of the problem.
The Remains Of The Expedition
After sleuthing around the city for a while, Reed manages to track down the lost expedition. He puts on a diving suit and finds them trapped in a cave underwater. Unfortunately, they're not able to give Reed much information about what's happening, as they've all gone completely insane.
The lead researcher, Professor Harriet Dough, found an ancient artifact called the Seal that made everyone go cuckoo bananas. They were then attacked by a group of Innsmouthers who stole the Seal and kidnapped Professor Dough. Reed comes to the conclusion that rescuing Dough may lead to answers about what the heck is going on.
He reports his findings to Throgmorton, who tells him that he should go to the fish market to investigate a mysterious group called the EOD.
Reed meets another two important individuals at the fish market, where the EOD is handing out free fish to the needy. First, there's Ebernote Blackwood, a member of an important family in town, who moonlights as a prophet of impending doom.
The other is an EOD representative named Anna, who won't give Reed any information unless he join the group. She offers to let him into the EOD if he can find out who's breaking into their storage room and stealing their fish.
After figuring out what was happening to their fish supply, he gets put in contact with a member of the EOD who wishes to defect from the group and escape the city. This member, named Fred, offers to give Reed info on the location of Harriet Dough. After getting him a way out of Oakmont, he tells you that if anyone knows where the Professor is, it's most likely Ebernote Blackwood.
More Fish People Problems
Reed arrives at Ebernote's office, only to find that it's been attacked by the KKK, who obviously hate Innsmouthers. Ebernote was taken, but he managed to escape by summoning Wylebeasts. Reed discovers that he went to yet another underwater cave.
Reed finds Ebernote, who's in pretty bad shape from fighting off the EOD. He's managed to find Dough, and reveals that both she and Reed are people known as the Chosen Few, who have strange visions, and will potentially be involved in an event that will either save or doom all of mankind.
Upon finding Dough, she's acting a little loopy, and is seemingly ready to die in order to play her part in a great cosmic event. The flood was actually the beginning of a potential apocalypse, as the sea was the barrier between this world, and the world of great beings who can easily destroy us all. A prophecy foretold that one of the Chosen Few would use the Seal to either close or open the gates that hold these old gods at bay.
Reed tries to leave the cave with the Seal, but passes out upon trying to do so. When he comes to, he's strapped to a hospital bed, Harriet Dough is dead, the Seal and Ebernote have gone missing, and Johannes van der Berg is standing there waiting for him to come to.
Rituals And Sacrifices
Johannes tells Reed that Ebernote likely has the Seal, and Reed manages to find him. He tells Reed that the visions will eventually drive him mad, and he offers to take his place as one of the Chosen using the Seal in a ritual. Of course, everything goes horribly wrong as it tends to do, and Ebernote ends up dead.
Reed goes to Johannes, but as luck would have it, he's dead as well. He was shot several times, and Reed is framed for his murder.
Reed finds the actual murderer, who was blackmailed into doing it after his family was kidnapped. That doesn't really matter though, as it turns out that Johannes is actually still alive. He faked his death to work from the shadows, and tells Reed that he needs to fulfill the prophecy.
How It All Ends
Reed can close the gate and save humanity for a few more centuries, but Johannes tells Reed that he needs to open the gate and end it all. It's also pretty heavily implied that Johannes may be some kind of omnipotent being, and is most likely The Yellow King.
After some more running around, fighting Mayan witch people, killing weird flesh monsters, and having some pretty wacky hallucinations, Reed finally arrives at the temple of Cthygonnaar where he has to make a choice about the fate about the world. From here, the story has three possible endings:
Ending #1: The One Where Everyone Dies
Reed chooses to open up the gates and releases the being known as The Hidden Daughter. As the gate opens, he gets sucked into a big tentacled gaping maw, and it looks pretty painful. A giant tidal wave then appears, and it looks like everyone is pretty screwed.
Ending #2: Choices Are For Suckers
Instead of doing anything, Reed decides to say, "screw it,' and uses the Seal to teleport back home to Boston. We then jump forward a few years into the future, where Reed is at a bar drinking, and looking pretty miserable. He's also grown a pretty sick beard. Everything mostly seems fine, until Johannes shows up with a copy of the day's newspaper with the headline "Catastrophic Flood". Then, right on cue, the bar is flooded, and it looks like making no choice is actually a pretty bad choice.
Ending #3: The Happy Ending.... Except You Die
Reed decides to restart the cycle, saving humanity. You place the Seal, and sacrifice yourself to basically reset the Cthulu clock. We then see Johannes standing on the same dock from the beginning of the game, as a boat arrives into the harbor, likely carrying another poor Chosen sad sack as the cycle goes on and on.