In January 1954 a United States Air Force Boeing C-97 Stratofreighter codenamed Vixen 03 takes off from the Buckley Naval Air Station in Colorado on a late-night flight transporting a top-secret cargo from the Rocky Mountain Arsenal to testing grounds near the Bikini Atoll in the Pacific Ocean. The plane never arrives in the Pacific, and, despite a massive four-month search by the Navy and Coast Guard, no trace of Vixen 03 is discovered.
The story then jumps forward 34 years, where Dirk Pitt, Special Projects Director for the National Underwater and Marine Agency, is vacationing with Colorado Congresswoman Loren Smith at her father’s cabin in the Sawatch Mountains. Pitt discovers some aircraft parts in the cabin garage and follows this lead until he intuits that there is an aircraft crash site in the local lake, Table Lake. Calling for his friend and Assistant Special Projects Director Al Giordino to fly in specialized NUMA equipment, they survey the lake and quickly find the wreck of Vixen 03.
Discovering clues found on the wreck, Pitt follows the evidence to retired Admiral Walter Bass, United States Navy, who was the commander who ordered Vixen 03 on its top-secret mission. Bass first denies any knowledge of the plane, but after Pitt convinces him that he really has found the wreck, the Admiral reveals that the plane was carrying a cargo of 16-inch battleship shells loaded with a deadly biological doomsday organism. The organism, nicknamed QD for quick death, is a virulent bacterial weapon that causes nearly instant death. The strain is described as being so deadly that just five ounces air-dropped over Manhattan Island would kill 98% of all human life, and, because the strain actually grows stronger over time, would render the island uninhabitable for up to 300 years.
Determined that this doomsday organism that he hoped was lost forever must never fall into the hands of the government that someday may decide to use it, Admiral Bass convinces Pitt, Admiral Sandecker and the rest of the NUMA team that they must secretly raise Vixen 03 and destroy the deadly cargo. The team raises the wreck and discovers that eight of the 36 shells are missing, apparently salvaged by local divers and sold to the Phalanx Arms Company. Pitt follows the trail and is able to recover six of the eight shells, but discovers that the last two were mistakenly sold as part of a large shipment to the African Army of Revolution.
The African Army of Revolution is an organization of black African militants led by expatriate American Hiram Lusana with the stated goal of overthrowing the minority white government of the Republic of South Africa using international public opinion and force against military targets. Pieter de Vaal, Minister of the South African Defense Force, is determined to stop the AAR and develops a plan to both rid himself of the AAR and topple the existing government and put himself in power.
The plan, code-named Operation Wild Rose, is a plot to use black mercenaries in a terrorist attack on the United States to discredit the AAR and win sympathy for the white minority government in South Africa. De Vaal recruits Captain Patrick McKenzie Fawkes, late of the Royal Navy, who believes his family was slaughtered by the AAR, to lead the plan. The audacious plan calls for Fawkes to take control of the former U.S. battleship Iowa, which was sold for scrap and purchased by an AAR holding company, to undergo a major gutting, raising her draft and allowing her to ride much higher in the water. Raising the draft enables Fawkes to sail the ship up the Potomac River and proceed with the plan for a terrorist attack by shelling Washington D.C..
With the help of Dale Jarvis, Director of the National Security Agency, Pitt discovers the plot to shell Washington with 16-inch battleship shells and, unbeknownst to anyone but Pitt and a few others, unleash the deadly QD organism on the nation’s capitol by accident. While the President and the Joint Chiefs launch a plan to take the ship and capture the shells intact, Pitt hopes to keep his promise to Admiral Bass and launches a daring mission of his own to destroy the QD warheads before they can be used, by the terrorists or the government.