For a three-act plot analysis, put on your screenwriter’s hat. Moviemakers know the formula well: at the end of Act One, the main character is drawn in completely to a conflict. During Act Two, she is farthest away from her goals. At the end of Act Three, the story is resolved.
Act I
Walter Moody comes to Hokitika one stormy evening, his ship (the Godspeed) almost wrecking before he can get onshore. On top of the bumpy ride, he saw something weird on board, so he's really looking forward to a nice calm evening at his hotel. However, he finds anything but relaxation when he heads into the smoking room and finds twelve men having some kind of mysterious powwow. They don't seem too happy to be interrupted, either.
However, they ultimately take Moody into their confidence and explain that some weird stuff's been going down in town that they're trying to clear up. It turns out that Moody himself has already become involved in their collective "story" without realizing it, as the man who captained his boat, Francis Carver, seems to be at the heart of the crimes and mysteries that the twelve men are trying to untangle, which include stolen treasure, gunshots, drug use, mistaken/stolen identities, fraud, a possible murder, a missing man (i.e., another possible murder), and a prostitute (and former opium addict) who had (apparently?) tried to commit suicide.
Once they're done talking, news comes that the Godspeed has wrecked.
Act II
As time progresses, the mysteries only get thicker. The prostitute who tried to take her life, Anna, is now living with Lydia Wells (Carver's girlfriend) and apparently has some history with her. The two women run a séance to summon Emery Staines, under the assumption that he is dead. Lydia seems to assume that, anyway.
Meanwhile, Anna's former dealer, Ah Sook, has history with Carver and has sworn to kill him as revenge. However, after finding him totally by accident in Hokitika (where he had settled after giving up on his original plan to kill Carver), Sook mistakenly came to believe Carver had left town.
After the séance, at which Wells pretends to channel Carver's spirit, Sook finds out that Carver is actually in town and starts making preparations to kill him. However, George Shepard kills him first. George had his own score to settle with Sook from Sydney (see the chapter-by-chapter plot summary for more on that).
While Sook's aborted revenge plot was playing out, Te Rau, a local Maori man, found Staines hiding, delirious and wounded, in Crosbie Wells's cabin. Aha! So that's where we left him…
Act III
Anna and Emery end up on trial, and Moody conveniently serves as their lawyer. Staines pleads guilty and is sentenced to nine months of hard labor, and Anna is acquitted.
The dishonest behavior of Carver and Lydia Wells (who had gotten married) came out at the trial, and when Carver was remanded into custody, someone (probably Te Rau) snuck into the carriage taking him to jail and killed him.
After the trial, Moody went out on an extended dig, just as his father showed up in town looking for him.