Plot
Flynn Carsen (Noah Wyle), a perpetual college student in his 30s with 22 academic degrees, [1] is kicked out of college by his professor, Harris (Mario Iván Martínez), who arranges for Flynn to get his 23rd degree mid-term. They have just completed a 1/20th scale model of the great pyramid, complete with a gold capstone. It will be months before he can sign up for another class. He tells Flynn—who does not know the names of his fellow students— that he lacks real-life experience and needs to see life outside of college. Flynn's mother, Margie (Olympia Dukakis), says the same thing. She is constantly worried about her son and encourages him to get a job, find a wife, and be happy.
Flynn receives an invitation to interview "for a prestigious position" at the Metropolitan Public Library. He is hired, and told that the position of Librarian has existed for thousands of years. His role is to protect historical and often magical items stored in a secret space far below the "real" library, including Pandora's Box, Tesla's Death Ray, the Holy Grail, the transmuted corpse of King Midas, and other things.
Flynn finds that the job entails more than he expected when one of three parts of the Spear of Destiny is stolen by a cult known as the Serpent Brotherhood, led by the former librarian Wilde (Kyle MacLachlan), who had faked his own death. (The audience learns of Wilde's involvement immediately.) Judson explains that whoever has the complete Spear of Destiny will control the destiny of the entire world (it is said in the film that "Hitler had only one" piece of the Spear). Flynn is the only one on Earth who can track down the remaining two pieces and prevent the Serpent Brotherhood from possessing all three. He heads off to the Amazon jungle, with only two tools: his mind and a book written in a previously untranslated language called the "Language of the birds.”
On the plane, Flynn is ambushed by members of the Serpent Brotherhood and is rescued by a woman who forces him out of the plane in mid-air. Once they land, he finds that his rescuer, Nicole Noone (Sonya Walger), has been sent by Judson. She works for the Library in the role later defined as Guardian. She fell in love with the last Librarian and blames herself for his death. She resists any friendly feelings for Flynn. As the two travel through the Amazon rainforest, they encounter waterfalls, headhunters, bridge collapses, and Maya death traps, which they manage to survive with little difficulty thanks to Flynn's extensive knowledge and Nicole's physical prowess. They retrieve the second piece of the spear and are immediately captured by the brotherhood and Wilde, who is about to shoot Nicole when Flynn steps in front of her. He makes a deal to find the last piece of the spear in exchange for Nicole's life. They head to Shangri-La, in the Himalayas.
At Shangri-La, they learn that their arrival has been prophesied. Flynn retrieves the last spear piece, the blade, and the temple starts to collapse. The monks battle the Serpent Brotherhood and Flynn and Nicole escape in a helicopter, which he flies somewhat erratically, using his book knowledge. They arrive at a hotel, where Nicole orders champagne and asks Flynn if he has read a lot of books about making love. Flynn wakes up the next morning to find Nicole, the spear blade and his clothes missing. Judson contacts him through a TV in the hotel lobby, and when he describes the conditions necessary to join the spear parts together—a golden-cap-stoned pyramid, augmented by a powerful electromagnetic field during a full moon—Flynn realizes that Professor Harris is in on the scheme. He tells Judson to call the Marines, he is coming home.
Judson meets him outside the university building where the pyramid was reconstructed, and when Flynn asks where the Marines are, Judson flashes a tattoo and replies “Semper Fi!” They watch as the Serpent Brothers, including Harris, assemble to watch Wilde call down the ancient powers and fuse the spear into one. Nicole is their prisoner. After Judson decks a henchman, he says to Flynn, “I was a Librarian, too, you know.” Wilde stabs one of his men, absorbing his life force through the spear, and starts for Nicole. Flynn tackles him and frees Nicole. Nicole and Judson take on the Brotherhood while Flynn follows Wilde, who tries to kill him. When the spear strikes stone the Pyramid shakes. Realizing what is happening, Flynn leads Wilde to damage the support stones, upsetting the precariously balanced structure. The capstone then falls onto Wilde, killing him. Judson and Nicole stand in a room full of unconscious people. Flynn reclaims the spear in the name of the Library, where it is displayed near Excalibur. Flynn draws the sword from its stone. Judson and Charlene show him the latest portrait in the gallery of Librarians: Flynn, holding the Spear.
Three months later, Flynn is at a café when Nicole informs him that the 'Deadly Scorpion League' has got their hands on a time machine. They take off, pursued by four members of said cult.
