U.S. National Underwater and Marine Agency (NUMA) Special Projects Director Dirk Pitt, who happens to be nearby, arrives at the site just in time to stop a group of 'tomb raiders' working for the Fourth Empire from destroying the chamber and stealing its curious artifacts. He also takes photos of the mysterious inscriptions covering the surfaces of the room. He also manages to save the lives of numerous people in danger of drowning in the chamber, which had been flooded with water.
One of the artifacts in question is an exquisitely carved skull of polished obsidian (see crystal skull). It seems unique, but curiously, another exists—in the private collection of a descendant of the whaling sea captain from the opening scenes of the novel.
When the descendant is confronted by the new skull, she shows them her treasure: an identical skull, and the log of the ship that found it. It pertains to an island somewhere in the south Indian Ocean, which was never properly explored.
The two skulls are handed over to NUMA for study and analysis. An argument develops in the organization as to whether or not they are Atlantean in origin.
Al Giordino and Rudi Gunn make it to the island and discover another inscribed chamber that housed the second skull, but discover another larger chamber beyond it. Here, they find perfectly-mummified, pre-Hellenistic men and women, surrounded by friezes of exotic cities and strange, mythic animals. They are ambushed by Fourth Empire thugs yet again, but manage to defeat them.
Meanwhile, Pitt is aboard an icebreaker in Antarctica searching for the 1770s merchant ship. The ship is found, but Pitt narrowly escapes disaster from an attack by a German U-boat that has been missing since 1945. The U-boat is destroyed by a US nuclear submarine and Pitt recovers the body of a beautiful female officer by diving to the wreckage.
At NUMA headquarters, the skulls have been examined. Inside both are geometrically exact globes. However, the continents are in different locations; Antarctica in particular is now almost temperate. Coastlines are also different, further out. The inscription symbols are fed into the computers, and translations are awaited.
Pitt returns to Washington and interrupts someone stealing the latest report from the NUMA director's office. After a brief chase, Pitt overcomes the thief and discovers a beautiful twin to the U-boat officer. Blood tests of both women show not only are they genetically identical, but their systems are so resilient as to allow them a long natural lifespan. The women are relatives, but not sisters. Both women are employed by Destiny Enterprises, a corporation based in Argentina, connected to Nazi escapees from Syria, and includes Fourth Empire Holdings. Pitt suspects foul play.
The next morning, the results are back. Apparently, the chambers are the work of a civilization calling themselves the Amenes (pronounced Ah-Meen-Eez). A nation of seafarers, traders, and wisemen, they discovered and traded with most of the world, leaving coastal towns wherever they went. However, a comet struck Earth at the end of the Pleistocene period, ending the Ice Age. This caused a world wide series of tidal waves which wiped out most of their civilization—and, thanks to the urbanization they had begun, most of their civilized contemporaries as well. The survivors were all in the uplands, and usually less advanced. However, some of the Amenes survived in isolated pockets. Banding together in a sort of priesthood, they tried to pass on their knowledge of the world, architecture, astrology, navigation, and history. However, the knowledge was transmitted inexpertly, and was twisted as a result. Depressed, the priests saved the bulk of their knowledge in a series of enclosed inland vaults, similar to the one found in Colorado, and then passed out of history.
But the comet which obliterated their society had a twin. According to their impressive mathematical models, the twin would return in some 9,000 years—in other words, soon—and produce similar results. The data is passed on to an observatory for analysis.
The Wolfs have created four superships to save themselves from the cataclysm, and everything required for a future civilization. Dirk Pitt and Al Giordino take a tour of one of the ships, while rescuing Pat, who was captured for her ability to decipher the Amenes inscriptions.
Around this time, Dirk meets Karl Wolf, the C.E.O. of Destiny Enterprises Limited. According to the references in the novel, he is a direct descendant of Ulrich Wolff, Colonel of the S.S. A tall, blond man of impressive build, he compliments Dirk on his luck. When Dirk mentions the potential catastrophe, and the loss of life it will entail, Wolf replies, "There is the difference between us, Mr. Pitt. You see this event as an ending. I see it as a new beginning. And anyway, my organization is already working on accelerating that timetable." Leaving them with this, he departs.
The data from the observatory comes back: the prophecy is false. Although the Amenes mathematical model was quite precise, computerized methods are faster and more exact. The comet is scheduled to return to Earth in another few millennia and miss the planet entirely.
Pondering Wolf's comment, NUMA researchers note that New Destiny is putting a lot of capital into a series of vast ships with which to survive the deluge. As well as this, information linked to a nanotech research facility in Antarctica comes to light. According to some sources, the facility is built on the ruins of an Amenes city found there by Nazi archeologists before World War II. It was intended as a submarine base, but never used.
The plan ultimately comes to light: the villains intend to use nanotechnology to separate the Ross Ice Shelf from the Antarctic mainland. The loss of such a large mass will destabilize the ocean currents of the southern hemisphere, and unbalance the planet (Pole shift theory). In the resulting wave of earthquakes and tsunami, the population would be decimated, and civilization would collapse.
Dirk and his friends travel there immediately, but their transport breaks down. They encounter a rich eccentric named 'Dad' (Clive Cussler) who is there with a team to recover the gargantuan Antarctic Snow Cruiser left there in 1940 during Admiral Byrd's third Antarctic expedition. Using the Snow Cruiser, they are able to make it the rest of the way to the villains' base in the ancient Amenes city. There, they deactivate the nanotechnology with minutes to spare, and the authorities arrive to secure the base.
They are then faced with the problem of the Wolfs. If placed on trial, the family would call upon influence from the governments of the world, most of whom owe them money. However, they cannot be allowed to walk free, as it would be far too dangerous. Dirk settles for offering them a choice between walking out of the base in the middle of a blizzard, or death by firing squad. Pausing to say they admire his style, the family departs. They die of hypothermia soon afterwards.
Upon return to Washington, D.C., Pitt and Giordino realize that their plane has been subtly replaced with a facade, piloted by Destiny Enterprises muscle. Landing at a small air field outside of D.C., Pitt and Giordino take control of the aircraft and literally drive the craft down the highways, eventually ending up in downtown D.C. Chased by a series of vehicles from the Wolfs, Al Giordino destroys both vehicles with weapons from the door of the aircraft. After being arrested by the D.C. Police Department, Pitt and Giordino were released to the White House where both meet with the President, his cabinet, Admiral James Sandecker, and Congresswoman Loren Smith.
[[[Atlantis Found|edit]]] Series continuityEdit
It is revealed in the book that 'Dad' is in fact Clive Cussler himself. That he appears in his own work is a recurring theme of the series. And as mentioned by Loren Smith, this is the first time where Dirk Pitt doesn't take back the form of transport used in the book (an old car/plane/boat etc.) to his hangar.