The film begins with a prologue set in Richmond, Virginia in 1865, showing the ironclad CSS Texas, carrying the last of the Confederacy’s treasury, as Captain Mason Tombs tries to run a Union blockade. The film then moves to the present day, where World Health Organization doctors Eva Rojas and Frank Hopper are investigating a disease that is spreading across Mali, Africa. Assassins, accompanied by a corrupt Tuareg named Zakara, attempt to murder Eva, but she is rescued by Dirk Pitt, from National Underwater and Marine Agency, who was diving nearby. Dirk gets a call from a dealer in Nigeria. He sells Dirk a gold Confederate States of America coin, one of supposedly only five in existence, which was found in the Niger River. Dirk believes that this is a clue to the long-lost Texas. He convinces his boss, James Sandecker, to let him, Al Giordino, and Rudi Gunn, from NUMA, take Sandecker’s yacht, the Calliope up the Niger River to search for the Texas. They give Eva and Hopper a ride, so that they can continue their investigation, for the WHO. Businessman Yves Massarde and dictator General Kazim, who controls half of civil-war torn Mali, try to stop the doctors from discovering the source of the “plague”. Kazim sends men to kill them and the NUMA team, not realizing their CIA and Navy background. Dirk, Al and Rudi survive the attack, but the Calliope is destroyed in the process. Rudi tries to get out of the country to get help while Dirk and Al go to rescue the doctors. They save Eva, and then the three try to get across the border, but are captured by Tuareg, who are fighting the civil war against Kazim. The Tuaregs’ leader, Modibo, shows Eva his people, who are dying from the same disease she was investigating at the beginning. After taking samples and analyzing them, Eva finds that their water is contaminated with toxins. By accident, Al stumbles into a cave with a painting showing the ironclad Texas. Dirk believes that the Texas became stranded when the river dried up after a storm and that the same river that carried the Texas now runs underground, spreading the contamination. They start to follow the dry river bed and work their way to the border. Dirk still hopes to find the ironclad along the way. Their plans are interrupted when they stumble upon a solar detoxification plant owned by Massarde, and realize that it is the source of the contamination. Rudi and Sandecker analyze their samples and find that the contamination is heading down the Niger River to the ocean and, if they don’t stop it in time, the toxins will reach the ocean and it will be devoid of all life. Not only that, they can’t get any government help to intervene during a civil war in a sovereign country. Massarde captures Dirk and Al, and keeps Eva while sending Dirk and Al to Kazim. They successfully escape but end up stranded in the middle of the desert. They find the wreck of a plane and rebuild it into a land yacht which they use to find civilization and contact Sandecker, who warns them that Kazim and his troops are after them. Dirk and Al enlist Modibo’s aid to return to the plant and rescue Eva. He helps them infiltrate the plant and rescue his people who are working there as slaves. Rather than risk discovery, Massarde plans to destroy the plant for good, making it almost impossible to stop the contamination. Al goes to defuse the bombs while Dirk tries to stop Massarde. After a fierce battle with Zakara, in which he is killed, Dirk manages to save Eva while Massarde escapes. Dirk, Eva, and Al get away from the plant in a 1936 Avions Voisin C-28, but they are attacked by Kazim in a helicopter gunship. A series of explosions along the dry river bed reveals the wreckage of the Texas, right where the cave painting showed it to be. They take cover inside thinking the ironclad’s armor will protect them but Kazim’s armor-piercing ammunition penetrates the rusted ironclad’s armor with ease. They manage to fight back with one of the Texas’s cannons and destroy Kazim’s gunship, just as Modibo arrives with Tuareg reinforcements which forces Kazim’s army to surrender and end the civil war. In the end the contamination is stopped, and Sandecker is offered a deal to do some covert work, while the government serendipitously funds NUMA, which he accepts, tentatively. It is heavily implied that Massarde is poisoned by his waiter, actually an undercover agent from the US government, while eating with another businessman. The Texas gold, which technically did not belong to the United States but to the CSA, is left with Modibo’s people. At the end of the film, Al is seen playing soccer with the local children. The cave, once empty, is now full of the gold. Later, while Al, Rudi, Sandecker are busy, Dirk and Eva are at the beach at her house on the bay in Monterey with Kazim’s newly repaired car.
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