In January 1954 a Boeing C-97 Stratofreighter of the United States Air Force, callsign "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 aircraft never arrives at its destination 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; Dirk Pitt, Special Projects Director for the National Underwater and Marine Agency (NUMA), 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 NUMAequipment, 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 aircraft, but after Pitt convinces him that he really has found the wreck, the admiral reveals that it 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 agent is described as being so deadly that just five ounces (143 ml) 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 (AAR) 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 by using international public opinion and force against military targets. Pieter de Vaal, Minister of Defense in the South African government, 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—and who believes his family was slaughtered by the AAR—to lead the attack. The plan calls for Fawkes to take control of the former U.S. battleship Iowa —which has been sold for scrap and purchased by an AAR holding company—and strip her down to raise her draft and allow 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 an 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 using Iowa' s 16-inch guns 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. When he does so, Pitt finds out – thanks to Captain Patrick McKenzie Fawkes, along with a few others – that Pieter de Vaal was behind the slaughter of his family. So, the U.S and the existing government arrange to have him become a 'cold case': a missing person. De Vaal is killed and buried in an unmarked grave – in the middle of nowhere – in Southern Africa.