In 1865, following the end of the Civil War, Thomas Gates and his son Charles Carroll Gates encounter John Wilkes Booth and Michael O'Laughlen, both affiliated with the Knights of the Golden Circle. They enlist Thomas, a master of puzzles, to decipher a Playfair cipher contained within Booth's diary. While O'Laughlen remains with Thomas, Booth departs to carry out his infamous assassination of President Abraham Lincoln. When Thomas deciphers the message, he realizes it reveals a route to Cíbola, the legendary City of Gold. However, chaos erupts in the streets following Lincoln's death. Suspicious of Booth and O'Laughlen's loyalty to the South, Thomas tears the diary's pages and discards them in a fire, just before O'Laughlen can eliminate him. O'Laughlen narrowly manages to rescue a fragment of the page before fleeing, while Thomas imparts his final words to Charles: “the debt that all men pay.”
Fast forward 140 years to the modern era, Benjamin Gates (played by Nicolas Cage), the great-great-grandson of Thomas, recounts his ancestor's tale during a Civilian Heroes conference. He and his father Patrick Gates are interrupted by Mitch Wilkinson, a black-market dealer who possesses a page from the diary that seemingly connects Thomas to Booth's and Lincoln's assassination. Seeking to honor his ancestor's legacy, Ben sets out to decode the cipher on the page.
Meanwhile, Special Agent Sadusky from the FBI grows suspicious of Mitch's sudden emergence with a rare Civil War artifact. Ben's tech-savvy friend Riley Poole just faces a setback when his Ferrari is impounded while he promotes his conspiracy books. They soon link the cipher to the Laboulaye Lady, which directs them to a hidden message on a scale model of the Statue of Liberty in Paris, a clue derived from Thomas's last words. This inscription reveals the location of two Resolute desks: one in the Queen's chambers at Buckingham Palace and the other in the Oval Office.
Unbeknownst to Ben, Mitch is shadowing his every move, utilizing a cloned phone belonging to Patrick to intercept their communications. In London, Ben discovers that Patrick has sent Abigail Chase (played by Diane Kruger), his ex-girlfriend, to assist them. Together, they sneak into the Queen's quarters, unveiling that the Resolute desk acts as a puzzle box, hiding a centuries-old plank with unreadable hieroglyphics. They photograph this before Mitch and his men snatch it during a high-octane car chase through the city. Patrick hints that this plank could lead to Cibola.
The story recounts history's attempts to find Cibola; when explorers set out in 1527, they failed to locate it. Ben persuades Patrick to contact Dr. Emily Appleton, Ben's mother and Patrick's former spouse. Emily can partially translate the plank, but the message remains incomplete. With Abigail's current boyfriend, Conner, connected to the White House, they devise a plan for Ben to access the Oval Office, where he discovers the desk compartment bare, except for a symbol resembling an eagle with a scroll—indicating the enigmatic Book of Secrets. Riley asserts the Book's reality, emphasizing it holds truths to numerous conspiracy theories, including the mysteries behind Watergate, Area 51, the Apollo program, and the assassination of President John F. Kennedy. Traditionally, only the sitting President has knowledge of the Book's location.
In a bold move, Ben organizes events to ensure the President’s birthday celebration is held at Mount Vernon, planning to trap him alone in a series of neglected tunnels to discuss the Book. Although the President warns Ben of potential kidnapping charges, he ultimately sympathizes with Ben’s mission and discloses the Book's whereabouts at the Library of Congress. As Ben, Abigail, and Riley search the Library, they find themselves surrounded by the FBI, including Sadusky.
Within the Book, they discover that Calvin Coolidge had previously stumbled upon the remaining segment of the plank in 1924, ultimately destroying it after taking a photograph preserved in the Book. He commissioned Gutzon Borglum to sculpt Mount Rushmore to erase pictorial evidence of the landmark indicated on the plank to safeguard Cibola's secret. As Ben's team evades the FBI, he sends an image of the plank to Patrick for Emily to interpret. Unbeknownst to them, Mitch intercepts this, coercing Emily to mislead Patrick regarding the inscription’s meaning, while subtly alerting him to the deception.
Arriving at Mount Rushmore prepared for a confrontation with Mitch, they soon realize that Mitch has leveraged Emily as a hostage. He compels Ben to pursue the final clues found in a vintage letter from Queen Victoria to Confederate General Albert Pike. Navigating a series of traps, they finally reach Cibola's concealed underground site, only to trigger a water surge from an upper lake that threatens their escape. The only way out is a drainage door that one person must manage to keep open. Initially forcing Ben into a sacrificial role, Mitch ultimately finds himself needing to hold the door while expressing regret for his earlier doubts. Mitch asks to share part of the glory of their discovery before Ben and the others make their escape.
Eventually, Ben and his friends are met by Sadusky and taken to a nearby military base. The President personally clears Ben of any wrongdoing, claiming he was inadvertently rescued. Soon after, the discovery of Cibola is announced, crediting Ben, his team, and Mitch for the find, ultimately vindicating Thomas Gates as a Civil War hero. As Patrick and Emily work side by side, eager to analyze Cibola post-drainage, Ben rekindles his romance with Abigail at Mount Rushmore, while Riley joyfully regains his Ferrari—“tax free.” The film concludes with a lingering mystery as the President requests Ben's assistance in deciphering the enigmatic Page 47.
