The novel begins in 1971 and introduces main character Malin Hatch and his older brother Johnny Hatch. In search for something to do with their summer day, Malin suggests that the two explore Ragged Island, an island owned by the Hatch family. Ragged Island is strictly off limits to the boys, because of its ability to "destroy" those who come in contact with it. The Hatch brothers ignore their father's demand to stay away from the island and set off for it. Once the boys make it to the island, a terrible accident takes place, that Malin will struggle with for the next 25 years.
Twenty five years later, Dr. Malin Hatch is approached by Gerard Neidelman, a self-proclaimed recovery specialist (a euphemism for treasure hunter), who claims to know who designed the pit, and, therefore, holds the key to unearthing the treasure. Hatch is at first skeptical of Neidelman's claim, but at length allows him to dig on the island.
Once on the island, things do not go as planned. Mysterious accidents, illnesses and computer problems plague the salvage team, and it is discovered that the architect of the "Water Pit" is more clever than anyone realized.
It also is revealed that the artifact, St. Michael's Sword, is in fact radioactive. This accounts for both the mysterious deaths of Red Ned's crew and for the computer glitches the team is having. The man who designed the water pit had realized that the artifact is actually deadly as well, so he built the pit to collapse on anyone entering it. However, the team learns too late that the entire island is sitting over a massive natural void in the ground, and that anyone removing the sword will collapse it. When Neidelman attempts to regain the sword, ignoring the warnings of the rest of the treasure-hunting team, he fatally irradiates both himself and another character before the island collapses beneath the sea and the sword is lost forever. Neidelman is also lost in the collapse.