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After discovering a communication capsule from the lost submarine Starbuck, Dirk Pitt is seconded from NUMA to the Hundred and First salvage fleet and ordered to help get to the bottom of the mysterious disappearance of the top-secret submarine. Pitt discovers that the submarine went missing in an area of the Pacific Ocean north of the Hawaiian island of Oahu nicknamed the Pacific Vortex. Similar in its mysterious reputation to the Bermuda Triangle, the Navy has documented 38 cases of ships vanishing without a trace with all hands in this area of the Pacific since 1956.

When the Starbuck originally went missing, the Navy conducted a massive and exhaustive search in the area of the Pacific where the submarine was last reported without finding a trace of wreckage. Pitt determines that it is suspicious that the Navy found no wreckage whatsoever, since the search pattern took them over the area that was reputedly the graveyard of the Pacific Vortex. Even if they did not find the wreckage of the submarine, they should have found some wreckage from any of the 38 ships rumored to have gone down in the area.

While doing research in an ongoing hobby effort to find the royal tomb of Hawaiian King Kamehameha, Pitt learns of the mythical island of Kanoli rumored to have existed north of the current Hawaiian Islands, and similar to the lost continent of Atlantis, rumored to have sunk into the sea killing the race of men who lived there. Pitt intuits that the Navy has been searching in the wrong direction and that they should turn around and concentrate their search for a sunken seamount in the area just north of the island of Oahu.

Pitt eventually discovers that in 1956 three respected men of science, Dr.'s Lavella and Roblemann, specialists in various areas of underwater science, followed the renowned Dr. Frederick Moran to their deaths in the same area of the Pacific. It is revealed that Moran, a renowned anthropologist and pacifist, who believes that it is only a matter of time before the human race destroys itself with the atomic bomb, has been searching for a place where he and his followers can survive the coming Apocalypse. Pitt believes that Moran and his followers discovered the sunken seamount that was once the island of Kanoli and have been using it as a base to raid Pacific shipping for the last 30 years as a means of financing their project.

When Pitt finds the sunken submarine in good condition, he determines that it cannot be immediately raised and also reveals the existence of the sunken fortress of Kanoli. The Joint Chiefs of Staff in Washington, DC elect to destroy the submarine with a nuclear tipped missile in an effort to ensure that its top secret design and nuclear missiles do not fall into the hands of Moran, the Soviet Union or any other nation. In an effort to stave off the attack, Moran kidnaps Adrienne Hunter, a long-ago love interest of Pitt and the daughter of the commander of the Hundred and First salvage fleet, Admiral Leigh Hunter. When Pitt discovers that Admiral Hunter will not tell Washington about the kidnapping of his daughter in order to delay the attack, he mounts a last-minute desperate rescue operation intended to rescue Adrienne and if possible snatch the submarine away as well.

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