The journal begins on Monday, September 13 at 5:30 a.m., with Ryan McCray in the hospital following a nearly fatal accident at the Dredge, the decaying remains of an old mining machine in the woods of Skeleton Creek. In his entry, he foreshadows the threat he and Sarah have discovered and the danger they face.

Ryan flashes back to the time just before his accident. He and his best friend, Sarah Fincher, decide to investigate the history of Skeleton Creek, fascinated by the macabre name. With the grudging help of the local librarian, Gladys Morgan, they make a series of discoveries at the local library: The town was originally called Linkford and was renamed to Skeleton Creek at the suggestion of the New York Gold and Silver Company. They find a series of newspapers called the Skeleton Creek Irregular that includes several unusual ads that refer to a group called the Crossbones and mysterious symbols that also appear at several places around town, suggesting a deeper mystery and conspiracy.

The trail of clues abruptly ended when New York Gold and Silver was bankrupted due to a series of lawsuits for environmental hazards.