The game begins with Silas (voiced by Phil LaMarr) sitting in his chamber, tightening a spiked metal cilice around his leg. He then picks up a handgun and leaves. The game cuts to Robert Langdon (Robert Clotworthy), a Harvard professor of symbology in Paris for a lecture, arriving at the Louvre, where he has been asked to view a crime scene by Cpt. Bezu Fache (Enn Reitel). Jacques Saunière (Neil Ross), Langdon's friend and curator of the museum, has been murdered. In flashback, Silas is shown asking Saunière where something is. Saunière tells him, and Silas responds, "I believe you. The others told me the same," before shooting him.

In the museum, Fache shows Langdon that before he died, Saunière wrote a numeric cipher and a message, "O Draconian Devil! Oh Lame Saint!" in blacklight ink. At this point, Sophie Neveu (Jennifer Hale), a member of the cryptography department arrives, explaining the cipher is part of the Fibonacci sequence, although the numbers are out of order. She then secretly tells Langdon he is in danger, as Fache thinks he is the murderer. In the toilets, she reveals the police have planted a GPS tracking device on Langdon. Neveu tells him that also written in black light ink were the words "PS. Find Robert Langdon." She explains that Saunière was her grandfather and "PS" was his nickname for her; "Princess Sophie." She believes that Saunière included the numerical cipher in the message to insure her involvement in the case.

Langdon throws the GPS device onto a passing car, and most of the police leave the museum to follow. He and Neveu return to the body, and Langdon realizes the numbers are out of sequence to tell them that the letters are also out of sequence; the words are anagrams. He deciphers "Draconian Devil" as "Leonardo da Vinci" and "Oh Lame Saint" as "The Mona Lisa". As they head to the painting, Langdon speculates "PS" could also refer to the Priory of Sion. His theory is strengthened when Neveu remembers seeing the letters together with a fleur-de-lis when she was a child; "PS" combined with a fleur-de-lis is the coat of arms of the Priory. At the Mona Lisa, they find a substitution cipher written in black light ink on the glass around the painting. The clues lead them to Saunière's office, where they listen to a message in which Sister Sandrine of Saint-Sulpice tells Saunière "the floor is broken and the other three are dead." A window is heard smashing and a man says, "Your fate was sealed the moment you stood against Manus Dei." As they continue to follow clues left by Saunière, eventually Neveu concludes they must head to his chateau. She and Robert split up as she heads to the chateau and he heads to Saint-Sulpice.

Once there, he finds a monk attacking a young nun. He knocks the monk out, and the nun, Sister Marguerite (Jane Carr), tells him that Sandrine is dead, killed by Silas, who was looking for something that Sandrine refused to give him. He left moments before the monks arrived, who seemed to be trying to erase evidence of his actions. Langdon concludes the monks are members of Sanctus Umbra, a militant subgroup of Manus Dei. Langdon examines the broken floor at the base of the Gnomon of Saint-Sulpice and finds a stone tablet with Job 38:11 inscribed on it; "Hitherto shalt thou come but no further." He deduces that Silas was misled by Saunière and the others. He heads into the crypt, where he finds a list of Priory Grand Masters, discovering Saunière was the current Master.

Meanwhile, at the chateau, Neveu heads for Saunière's underground grotto. She evades both Silas and the police, and follows a series of clues to find a key with the address of the Depository Bank of Zurich. Meeting up with Langdon, they head to the bank, where they open Saunière's deposit box, finding a cryptex. They then head to Château Villette, the residence of Sir Leigh Teabing (Greg Ellis), Langdon's friend and one of the world's foremost experts on the Holy Grail. Teabing and Langdon explain to Neveu that the Grail is not a cup, but a reference to a woman. Looking at da Vinci's The Last Supper, Teabing explains the image of John is actually Mary Magdalene, to whom the historical Jesus was married. This marriage was suppressed by the early Church, who needed its followers to believe Jesus was divine. Teabing explains that the chalice that held the blood of Christ, the Holy Grail of legend, was Mary herself, as she was pregnant with Jesus' child. At this point, Silas arrives, revealing he murdered Saunière under the orders of "The Teacher." Langdon and Neveu incapacitate him, and with Teabing and his servant Remy (Andres Aguilar), they head to London, taking the unconscious Silas with them.

Landing at Biggin Hill, they head to Temple Church. Langdon and Teabing go inside, but in the courtyard, Neveu sees Remy betray them and send a gang of thugs in after them. Langdon wakes up in a dungeon, but manages to escape, and meets up with Neveu. He tells her Remy is holding Teabing hostage to use him as a bargaining chip for the cryptex. Inside the church, Remy and Silas confront Langdon and Neveu, who flee and head to Westminster Abbey, where Teabing is being held. Once there, they decide they must solve the cryptex to bargain for Teabing's life. Following a series of clues left by Saunière, they do so, but before they can open it, they are captured by Remy. He takes them to Teabing, who reveals himself to be The Teacher. He shoots Remy as he no longer needs him, and reveals Silas has just been arrested for the recent murders. He tells Langdon and Neveu the Priory was supposed to make public the contents of the cryptex on the eve of the New Millennium, but Saunière decided against it. As such, Teabing determined to reveal the documents himself. He asks Langdon and Neveu to join him in revealing the truth about Mary Magdalene, but they refuse and Langdon destroys the cryptex. Teabing is arrested as he laments the truth being lost forever.

However, Langdon had removed the document before destroying the device. Following the clue contained within, he and Neveu head to Rosslyn Chapel. There, they find a family tree for the Saint-Clair family, running back to the Merovingian dynasty. In a series of documents, they learn that when Sophie's family were killed in a car accident, newspaper reports said that all of the family were killed; mother, father, and two children. The reports also state the family's name was Saint-Clair. Langdon realizes the truth; Neveu survived the accident, and the Priory put out the story she was dead to protect her, as she is a living blood relative of Jesus. Neveu's grandmother then arrives, explaining the family changed its name for protection. She introduces Neveu to her brother, who also survived the crash; he came to Scotland whilst Neveu went to France with Saunière. Neveu's grandmother then tells Langdon that the grail is not in Rosslyn, it is in France. He realizes the clue in the cryptex didn't point to Rosslyn but to the Rose Line in Paris. He says goodbye to Neveu and heads to France, finally understanding the grail lies beneath the Louvre Pyramid.