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Sahara
In 1865, at the conclusion of the American Civil War, Richmond, Virginia is in ruins. The CSS Texas, captained by Mason Tombs is loaded with the last of the Confederacy 's gold to keep it from Union forces before disappearing.
In present day Mali, there is a civil war between dictator General Kazim and the Tuareg people. In Nigeria, WHO doctors Eva Rojas and Frank Hopper investigate a disease affecting people who have been in Mali. Zakara, a corrupt Tuareg, tries to murder Eva, but she is rescued by Dirk Pitt, from the National Underwater and Marine Agency, who was diving nearby.
Dirk gets a gold Confederate coin found in the Niger, a clue to the location of the long-lost Texas. He borrows his boss Sandecker's yacht to search for it. His partners Al Giordino and Rudi Gunn from NUMA accompany him. They first transport Eva and Hopper to Mali so they can continue investigating the disease, then continue up the Niger. While taking water samples, they discover red algae, which puzzles them as it is not usually found in fresh water.
Kazim, with businessman Yves Massarde, try to stop the doctors from discovering the source of the disease. Kazim sends men to attack the yacht. Dirk, Al and Rudi survive, but the yacht is destroyed. Rudi leaves to get help while Dirk and Al go to rescue the doctors.
Kazim's men track down the doctors and kill Hopper. Dirk and Al rescue Eva. As they are trying to leave Mali, they are captured by the Tuareg insurgents. Convincing the group that they are hunted by Kazim, their leader, Modibo, shows Eva his people dying from the disease she is following, which she determines is a waterborne toxin with no available treatment or cure. Al stumbles into a cave with a painting showing the ironclad Texas. Dirk believes that the Texas became stranded when the river dried up and the same river that carried the ship now runs underground.
Following the river bed, they stumble upon Massarde's solar plant, which they discover is the source of the contamination. Meanwhile, Rudi and Sandecker have deduced that chemicals are creating the red algae and seeping slowly towards the Atlantic Ocean, where they will expand rapidly upon entering salt water and kill ocean life worldwide. Despite this, the US government is reluctant to intervene. Dirk, Al and Eva infiltrate the solar power plant on an inbound train. However, Massarde and Zakara capture them, keep Eva, and send Dirk and Al in a truck to Kazim. Dirk and Al escape in the middle of the desert and rebuild a plane wreck into a land yacht; make contact with Sandecker by telephone, they learn of the impending disaster.
Dirk and Al return to the solar plant, with Modibo's help. To cover up the existence of the waste, Massarde plans to destroy it with explosives. Fearing the plant's destruction would guarantee worldwide water contamination, Al goes to remove the explosives while Dirk tries to rescue Eva. Dirk kills Zakara after a fight, but Massarde escapes via helicopter. Al successfully neutralizes the explosives.
The three leave the plant in an Avions Voisin C-28 stolen from Kazim by Modibo; the general pursues them in an attack helicopter, with his army following. A series of explosions along the dry river bed reveals the wreckage of the Texas. The trio hides in the armored ship, but Kazim's helicopter uses armour-piercing ammunition. Using one of the Texas ' s cannons, they manage to destroy the helicopter, killing Kazim. Modibo arrives with Tuareg reinforcements, forcing Kazim's army to surrender.
The plant is shut down, stopping the source of toxic waste. Sandecker agrees to work covertly for the US government in exchange for NUMA funding. The Texas gold is left with Modibo's people. It is implied that Massarde is poisoned by Carl, an undercover CIA agent, while Dirk and Eva start a relationship.