It was stated in the first film's commentary that there were no plans for a sequel, but due to the first film's impressive box-office performance, earning $347.5 million worldwide, a sequel was given the go-ahead in 2005. It took just 38 days of release for the sequel to out-gross the original.
The film premiered in New York City on December 13, 2007 and was first released in Korea and Taiwan on December 19, 2007. It was then released in Australia and the Middle East on December 20, 2007. The film opened in the United States, Canada, Japan, Spain, and Italy on December 21, 2007. It was released in Germany and The Netherlands on January 24, 2008 and in the United Kingdom and Denmark on February 8, 2008.
On April 14th 1865 in Washington D.C., five days after the Civil War, John Wilkes Booth and Michael O'Laughlen enter a tavern and approach Thomas Jefferson Gates and his son Charles Carroll Gates. They ask Thomas, a skilled puzzle-solver, to decode a Playfair cipher written in Booth's diary. O'Laughlen stays with Thomas as Booth leaves for Ford's Theatre to assassinate President Abraham Lincoln. Booth shots Lincoln, he jumps onto the stage and shouted "Sic semper tyrannis" (Latin for "Thus always to tyrants") at the audience before escaping. Just as Thomas discovers the coded message is a map to Cíbola, the Lost City of Gold, he realizes O'Laughlen and Booth are both members of the KGC and still loyal to the Confederacy. O'Laughlen threatens him, Charles witnesses the trouble as chaos news of Lincoln's assassination arises in the streets. The moment O'Laughlen got distracted, Thomas rips pages from the diary and burns them in a fireplace, and then O'Laughlen shot him. O'Laughlen only manages to save a partial page from the fireplace before escaping, while Thomas' dying words to Charles as he holds his hand are "the debt that all men pay."
140 years later, where Benjamin Gates, Thomas' great-great-grandson, is retelling Thomas' story at a Civilian Heroes conference how Thomas burned the 18 pages from Booth's diary to prevent the KGC from finding the vast treasure of gold otherwise the Union would have lost the Civil War to the Confederacy. He and Patrick are publicly accosted by Mitch Wilkinson, a black market dealer who comes in possession with one of the missing pages from Booth's diary (the one pull out of the fire), which appears to link Thomas to Booth and Lincoln's assassination. Accused as a conspirator, Ben sets out to solve the puzzle from the page to prove his family's innocence.
Meanwhile, Peter Sadusky of the FBI finds it suspicious that a black market dealer like Mitch would suddenly come forward with a rare civil war artifact. Riley became a novelist and was giving out his Templar Treasure books when his Ferrari just got impounded by the IRS because of an unexpected debt then later meets up with Ben. They head for Ben's mansion to infiltrate, since Ben and Abigail haven't been getting along due to his 'assuming way of talking', and then Ben bribes Abigail with the Boston Tea Tables to let them use her ID card to access the Booth diary page.
After several hours of spectral imaging, they discover the cipher on the diary page. Thanks to Thomas' last words that Patrick heard from Charles they know the key code is "Death" and then decoded part of the cipher that says "Laboulaye Lady" as in Édouard Laboulaye who was a Freemason and had the idea for the scale model of the Statue of Liberty. In Paris, Ben and Riley found an inscription engraved on the Île aux Cygnes, referring to the two Resolute desks. They head for London to look at the desk at Buckingham Palace in the Queen's chambers. Ben unaware Mitch is tracing his footsteps, using a clone of Patrick's cell phone to intercept messages. Patrick has sent Abigail to help. They are able to infiltrate the Queen's quarters by creating a fake argument and Riley who had previously hacked into the security system, and found the Resolute desk. They discover that it acts like a tumble safe made by Malcolm Gilvary, a puzzle box designer in 1880. Using the 4-digit combination: 1876, reveals a hidden compartment with a five centuries-old plank of wood and indecipherable hieroglyphics on it. Leaving the palace unseen by setting off the fire alarm and jamming the video monitors, Mitch and his men caught up to them and engage in a car chase throughout London. Ben manages to photograph the plank via a traffic cam before Mitch and his men steal it. Back in Washington D.C., Patrick indicates the Native-American plank leads to Cíbola, the City of Gold.
Ben convinces Patrick to help them arrange a meeting with Dr. Emily Appleton, Ben's mother and Patrick's ex-wife at Maryland University. Emily is able to translate the plank but states that the glyphs are partial, leading Ben to conclude a second plank must be hidden in the other Resolute desk in the Oval Office of the White House. Abigail coax her current boyfriend Conner, a curator of the White House, to invite them inside the Oval Office during an Easter Egg Roll, but Ben finds the Resolute desk compartment empty, though he does find a stamp bearing the seal (eagle clutching the scroll) representing the supposed "Book of Secrets." Riley asserts the Book is real, having just written its existence himself as he unraveled the seal from the Freedom of Information Act (FOIA) into his books. Claiming it contains collection of controversial documents, and the truth behind government conspiracy theories such as: the 18½ missing minutes of the Watergate tapes, whether aliens are being held in Area 51, proof if the Apollo 11 really landed on the moon, and the mystery of JFK assassination. Leading them to believe whatever was on the plank is now in the Book of Secrets. Sadusky confirms Ben, however, the Book is for presidents' eyes only and the current President himself knows the whereabouts of the Book. As Ben empathizes on how Lincoln and Thomas Gates gave their lives to bring the United States into 'one nation', he made a decision to kidnap the President, knowing the President cannot answer anything regarding the Book of Secrets while in public or surround by bodyguards.
Ben and his team manipulate events to assure that the President's birthday celebration occurs at Mount Vernon, allowing Ben to sneak in and lures the President to a set of George Washington's disused tunnels. Ben then blocks off the entrance, trapping the President alone with him so they can talk about the Book of Secrets. Though the President warns Ben that he will be charged for federal offense, he is sympathetic to Ben's case and provides him with the Book's location at the Library of Congress, then go their separate ways through the exit. Rushing to the library, Ben, Abigail, and Riley locate the Book's index code in a secret locked panel. In the Book, Queen Victoria knew the truth about Cíbola, and sent two coded missives to the Confederacy; one was the Playfair cipher in Booth's diary in order to help a "divided" America. Then they find a photograph of the missing plank that was found by President Calvin Coolidge in 1924 and then destroyed. Coolidge had also commissioned Gutzon Borglum to carve Mount Rushmore to erase the landmark indicated on the plank in Black Hills, South Dakota, as a cover-up to protect the City of Gold. FBI including Sadusky surrounds the building. As Ben and his team narrowly elude the FBI, he sends an image of the plank to Patrick to give to Emily to translate; unaware Mitch has intercepted this and is waiting for Patrick. Mitch forces Emily to lie about the inscription's meaning to Patrick, but is able to give him a non-verbal cue of this falsehood.
Ben, Patrick, Abigail, and Riley arrive at Mount Rushmore, prepared to deal with Mitch, but find Mitch has brought Emily along, using her as a hostage to ensure Ben follows the final clue on an old letter sent from Queen Victoria to Confederate General Albert Pike whom Mitch is descended from. They are able to find a noble bird that is revealed under a cloudless rain on an island of stone and pulls a latch which opens the secret entrance, and the group avoids several traps before arriving at the underground site of Cíbola, the City of Gold! As they explore, they accidentally cause the cave to flood with water from a lake above. The only means of escape is through a drainage door that must be held open on one side to allow the rest to escape and closed afterwards, trapping the one controlling the door. Mitch initially forces Ben to sacrifice himself, by threatening Abigail, but after a surge of water, Mitch finds himself holding the door open. He apologizes to Ben for framing his family, and requests that part of this discovery be in his name. Mitch drowned; Ben and the others escape safely.
Ben and his friends are met by Sadusky and taken to a nearby military base. Ben is cleared of kidnapping by the President himself, who claims that Ben rescued him after the tunnel they were in closed accidentally. Sometime later, Cíbola is announced with Ben, his team, and Mitch Wilkinson given credit for its discovery. Thomas Gates is proved a Civil War hero. Patrick and Emily, happily working together, eagerly take to the task of analyzing Cíbola once it is drained of water. Ben and Abigail rekindle their relationship at Mount Rushmore's fireworks, and a girl praised Riley's Templar Treasure books. Riley arrives home to find that the President has given his Ferrari back "tax free." The only mystery remains is what the President requested Ben to decipher on Page 47 of the Book. Ben replied as a "Life-altering" message.