The film opens with a gripping prologue set in Richmond, Virginia, in 1865, showcasing the ironclad CSS Texas as Captain Adrian Tombs, played by Robert Cavanah, attempts to navigate through a Union blockade while carrying the final treasury of the Confederacy. Fast forward to the 1990s, where World Health Organization doctors, Eva Rojas and Frank Hopper (Glynn Turman), are on a mission to investigate a mysterious disease wreaking havoc in Mali, Africa. Just as Eva’s life is threatened by assassins, she finds a savior in Dirk Pitt from the National Underwater and Marine Agency, who was operating in the area.
Dirk receives a tip from a dealer in Nigeria, unveiling a rare gold Confederate coin, one of just five known to exist, discovered in the Niger River. This leads Dirk to suspect that it might be a clue to the whereabouts of the long-lost Texas. Persuading his superior, James Sandecker (William H. Macy), he coordinates a mission to Mali alongside Al Giordino and Rudi Gunn (Rainn Wilson), bringing along Eva and Hopper to further their WHO investigation.
The storyline intensifies as businessman Yves Massarde (Lambert Wilson) partners with the oppressive dictator General Kazim (Lennie James), who rules over war-torn Mali, making efforts to halt the doctors’ inquiry into the epidemic. Unbeknownst to Kazim, Dirk and his team secretly possess CIA and Navy expertise, allowing them to survive a deadly assault. Rudi attempts to exit the country for aid while Dirk and Al engage in a daring rescue mission for the doctors. After a series of harrowing encounters, they manage to save Eva from enemy hands. However, they soon find themselves captured by the Tuareg, who are entrenched in the civil conflict.
Within the turmoil, the Tuareg leader, Madibo, reveals to Eva the dire condition of his people. After analyzing the area, she discovers that their water source is heavily polluted. In an unexpected turn of events, Al stumbles upon a cave depicting the ironclad Texas. Inspired, Dirk theorizes that the Texas became trapped when the river's water receded, leading them to investigate the dry riverbed that parallels their quest for the ironclad.
Their journey hits a snag when they discover the solar detoxification plant owned by Massarde as the root of the contamination. Despite their attempts to secure governmental assistance, red tape due to the ongoing civil war stalls their progress. In a shocking twist, Massarde captures Dirk and his companions, keeping Eva hostage while sending Dirk and Al to Kazim. They manage a daring escape and reach out to Sandecker, aware of the impending threats from Kazim’s forces.
With Madibo’s support, they strategize a return to the plant for Eva’s rescue, also liberating the oppressed workers. In a race against time, they confront the impending destruction of the plant by Massarde. A chaotic skirmish ensues with explosions tracing the dry riverbed, unveiling the Texas just as depicted in the cave painting. They take refuge inside, fighting back against Kazim's aerial assault. The combination of resilience and collaboration leads them to defeat Kazim's forces, bolstered by Madibo and his reinforcements.
Ultimately, the contamination crisis is resolved, and Sandecker finds himself with new covert opportunities, as the government reluctantly supports NUMA. Massarde, oblivious to the turn of events, finds himself poisoned by his own negligence. The Confederate treasure is entrusted to Madibo’s people, leading to a tranquil conclusion where Dirk and Eva share a peaceful moment at her beach house, embodying the triumph amidst chaos.
