Young professor Robert Langdon is pulled into a complex mystery when his beloved mentor, Peter Solomon, is kidnapped; armed with knowledge of history and symbols, Langdon must work together with Peter's daughter and other allies to save him.

Langdon and Katherine encounter Peter's Freemason friend Bellamy who agrees to help them in their hunt for the capstone. Thinking Peter's ring holds the decryption key for the Bible page, they go to the hospital seek out the help of Nuñez hoping he can get that they need from into the evidence room. Katherine laments that she may never be able to reconcile with her father. Mal'akh threatens Langdon to get rid of Katherine, or he will.

Sato confesses to Bellamy that she was Zach's CIA handler. Bellamy tells her the story of a rogue Leviathan Group member who accessed the ancient wisdom 100 years ago and learned how to affect matter with his mind. On their hunt for the capstone, Langdon and Katherine instead find a mysterious, old 16mm film of the man - and the incredible event - that Bellamy spoke of. Peter, still in the Araf, experiences the death of his son, Zach, at his own hands. Nunez finds the body of Trish, who has been murdered by Mal'akh to send a message to Langdon: Don't disobey me again.

After recovering the capstone, Langdon is rescued by Nuñez at Wiggington Quarry. Katherine receives what she believes to be a psychic message from her father, giving her proof of life, as well as much needed motivation to fight on. Sato receives more information about the man she believes to be Mal'akh and teams up with Katherine, but her true loyalties remain in question.

Langdon uses an inscription on the stone box that enclosed the capstone to lead the team to an engraving at the National Art Gallery, but is still unable to find a map to the portal. Mal'akh sends Langdon video evidence that Peter is still alive, which provides further validation for Katherine. At Sato's urging the team decides to set up a secret fake drop to get Peter back, but the CIA ruins their strategy, leading to Langdon's abduction by Mal'akh. Meanwhile Nuñez finds himself in the clutches of the Janitor's wife Mina, who is revealed to also be a follower of Mal'akh.

After being captured by Mal'akh, Langdon is finally reunited with his mentor, Peter. Katherine tracks down Mal'akh's lair by watching Peter's hostage tape again and again. In the process of escaping from Mal'akh with Langdon, Peter glimpses something familiar in his captor's eyes and realizes Mal'akh has been Zachary this whole time. He shares the information with a shocked Sato. To avoid being caught, Mal'akh jumps off a cliff to his presumed death. But in truth, he's alive and has been arrested by the CIA.