The book, Cyclops, by Clive Cussler, is a techno-thriller featuring well-loved protagonist, Dirk Pitt. The story opens with the puzzling events aboard the Cyclops, a Navy collier, in 1918 with a captain who drinks more than he works and a strange cargo with equally strange passengers that board in Rio de Janeiro. The Cyclops has been issued a no communications order by the Captain and refuses to answer a distress call from Crogan Castle fifty miles away, near the northern coast of Cuba. Shortly after, the Cyclops encounters a similar rogue wave that the Crogan Castle had mentioned; only the Cyclops did not survive. Her secrets lie deep under the water with her.

Dirk Pitt is participating in a seaboard marathon near the Bahamas when a runaway blimp crosses his path and threatens the lives of the people on the beach and in the hotel. His desire to save perfect strangers embroils him in a plot that has bigger secrets than any he has ever encountered before. His ability to see through subterfuge, his calm in stressful situations, and his unique way of approaching problems make Pitt the perfect addition to a plot that threatens possession of the moon, of Cuba, and the very principles and strengths of America.

Because of his vast aircraft experience combined with his NUMA expertise, Pitt is a logical choice to retrace the route last taken by financier Raymond LeBaron. It is his blimp that appeared in front of Pitt during the race, and now Pitt is a passenger, heading toward what he believes to be sunken treasure. He believes they are looking for the Cyclops, and her treasure aboard, the La Dorada. Instead, he, Giordino, and Gunn are deceived by Jessie LeBaron, who pilots the blimp. They are taken close to the shores of Cuba. where they are attacked by Cuban military and fall into the ocean. They are prepared for this event, and while they are in the vicinity, they dive down to the Cyclops to see if her treasure is still aboard. It is not.

Back on the surface, they face a hurricane, a treacherous boat ride to a nearby island, and a very unfriendly greeting from the Soviet military who are part of a top secret military installment on an island just a couple hundred miles off the coast of Florida. Pitt escapes back to the U.S. and returns with military aid. They are just in time to save the lunar colonists who have secretly created Jersey Colony on the moon, a colony the Russian intend to seize. The Russians are foiled on the moon, and then Pitt further ruins their plan by reaching the space shuttle before she attempts to land in Cuba and be shot down by friendly fire. Once his friends are rescued, Pitt and Jessie head back to the military ship, but Jessie has other ideas and with a gun at his chest, they turn toward Cuba.

In Cuba, there is a Soviet plot to assassinate Fidel Castro and his brother Raul. Once the two men are out of office, the Russians intend to take over Castro's regime and establish a Soviet foothold in the Western Hemisphere. Their plot intends to blow up Havana Harbor and most of Havana, then blame it on the United States. Because Dirk Pitt is involved, the Russian plan does not go as planned. There is an explosion, and while it does kill a few people, it does not cause the vast devastation that is required for the Soviets to take over Cuba.

Finally, Pitt is able to continue his search for La Dorada, the fabled female statue that is to have the heart of a ruby and a head and hair of an emerald. Raymond LeBaron is known to have taken La Dorada to Cuba, and hidden her there. Once Pitt saves the world, he can finally finish his initial task of locating La Dorada.