Jacques Saunière, the Louvre's curator, is pursued through the Grand Gallery by an albino Catholic monk named Silas, who demands the location of the Priory's "keystone" to find and destroy the Holy Grail. Saunière gives him a false lead and is murdered. When the police arrive, they find his body posed like Da Vinci's Vitruvian Man. The police captain, Bezu Fache, sends his lieutenant, Jérôme Collet, to summon American symbologist Robert Langdon, in the midst of signing autographs after one of his public talks, to examine Saunière's body.
At the museum, Langdon is shown the body, and a secret message, readable only by blacklight, that contains an out-of-order Fibonacci sequence. Sophie Neveu, a police cryptographer and Saunière's granddaughter, reveals to Langdon that Fache planted a tracker on him after finding the words "P.S. Find Robert Langdon" at the end of Saunière's secret message, leading Fache to believe Langdon murdered Saunière. The two get rid of the tracker, distracting the police, and sneak around the Louvre, finding more clues in Leonardo da Vinci's works, eventually leading to Langdon to deduce that Saunière was the grand master of the Priory of Sion.
Silas is revealed to be working for an anonymous person named the Teacher, along with members of Opus Dei, led by Bishop Aringarosa. Evading the police, Langdon and Sophie travel to the Depository Bank of Zurich, where they access a safe deposit box of Saunière's, using the Fibonacci sequence. Inside the box is a cryptex, a cylindrical container that can only be safely opened by turning dials to spell a code word, and which contains a message on papyrus. The police arrive outside and Langdon and Sophie are aided by the bank manager, Andre Vernet, only for him to attempt to take the cryptex and murder them. Langdon disarms Vernet and flees with Sophie and the cryptex.
The two visit Langdon's friend, Sir Leigh Teabing, a Holy Grail expert who walks using crutches, who claims the Grail is not a cup but instead Mary Magdalene, Jesus Christ's wife. Teabing argues that she was pregnant during His crucifixion, and the Priory was formed to protect their descendants. The Opus Dei have been trying to destroy the Grail to preserve the credibility of the Vatican. Later, Silas breaks into Teabing's house, but Teabing, using one of his crutches, disables him. The group escapes to London via Teabing's private plane, along with his butler, Remy Jean. They travel to the Temple Church, but the clue to unlocking the cryptex is a red herring. Silas is freed by Remy while claiming to be the Teacher and taking Teabing hostage, dumping him in the car trunk, and taking Silas to hide out in an Opus Dei safe house. Teabing later poisons Remy and sends the police after Silas. Silas is shot by police after accidentally wounding Aringarosa, who is promptly arrested by Fache, who resents being used to hunt Langdon.
Langdon and Sophie are confronted by Teabing, who is revealed to be the Teacher, and who wants to bring down the Church for centuries of persecution and deceit. The trio goes to Westminster Abbey to the tomb of Isaac Newton, a former grand master of the Priory. Teabing demands that the pair open the cryptex. Langdon tries and then tosses the cryptex into the air. Teabing dives for it, catches it, but acid dribbles and the papyrus thought destroyed. The police arrive to arrest Teabing, who realizes Langdon must have solved the cryptex's code and removed the papyrus. The code is revealed to be "APPLE", after the apocryphal myth of the apple which led Newton to discover his law of universal gravitation. The clue inside the cryptex, which tells of the Grail hiding "'neath the rose", leads Langdon and Sophie to Rosslyn Chapel in Scotland.
Inside the chapel, they discover Magdalene's tomb has been removed. Langdon, after searching through documents, realizes that Sophie's family died in a car crash, that Saunière was not her grandfather but her protector, and that she is the last descendant of Jesus Christ. The two are greeted by several members of the Priory, including Sophie's grandmother, who promises to protect her. Langdon and Sophie part ways, the former returning to Paris. While shaving, he cuts himself and has an epiphany when his blood curves down the sink, reminding him of the Rose Line. Realizing the true meaning of the cryptex clue, he follows the line to the Louvre, concluding the Holy Grail, the sarcophagus of Mary Magdalene, is hidden below the Pyramide Inversée. Langdon kneels above it.