After persuading her that she wants to find the truth and help, Imelda allows Nico to access Carchon's room, which contains an elephant carving exactly the same as that of Nico's father and a stone cylinder, which contains a hidden code of letters. On Carchon's corpse, Nico discovers a ticket stamped "Bateaux de la Conciergerie" and goes to investigate the dock. By using the letters on the cylinder, she discovers a secret office area where Carchon and many others met for business. After writing her story up and publishing it, her editor tells her to drop the story at which Nico becomes angry. However, she receives a mysterious phone call from a man called Plantard who tells her he needs to speak to her about her story.
The next day, an American tourist George Stobbart enjoys a coffee at a Parisian cafe and sees an old man entering the cafe with a briefcase. Almost immediately, a clown arrives with an accordion, who steals the man's briefcase and drops his accordion. The accordion detonates and blows the cafe up. George manages to survive and investigates the cafe. He is soon interrogated by Augustin Rosso, a renowned police inspector who utilizes psychic techniques to question witnesses. George then meets Nico outside the cafe taking pictures, who explains that she was meant to meet the old man, Plantard. After agreeing to help with her story, George traces the clown's steps to the nearby sewers. Acquiring the clown's nose and a scrap of material, he exits the sewers and meets a war veteran, who explains a man exited the sewers before with a briefcase. Showing the scrap of material prompts the veteran to reveal the killer dropped his jacket and gives George the tailor's name and phone number. George attempts to find out more from the tailor, Todryk, but without the killer's name, Todryk is uncooperative.
George goes to Nico's apartment and she discovers an address inside the clown's nose for the costume shop where it was purchased. George goes there and learns the killer's name, Khan and that he hired both a clown and a pixie costume. Todryk then tells George of the Hotel Ubu, the killer's accommodation. Outside the hotel are two shady characters, Flap and Guido, who search George's pockets searching for something important. With the help of an English aristocrat, Lady Piermont, George obtains an ancient manuscript from the hotel safe, which Khan deposited. While infiltrating Khan/Mourlin's hotel room, he also finds a matchbook from the Club Alamut, which seems Middle Eastern. After evading Flap and Guido who are searching for the manuscript and returning to Nico, she deduces the manuscript is related to the Knights Templar, a wealthy and powerful order of knights wrongly accused of heresy and burned at the stake by the Inquisition. The plan was hatched by Philip IV of France and Pope Clement V in a bid to gain the Templars' amassed wealth but the treasure remained hidden. On the manuscript, there are several pictures: A knight with a sword and a bull, between them a gem is balanced on a tripod; A knight with a crystal ball; A man weaving on a loom with a ship in the background; a woman looking at a looking glass to see three bearded faces. Seeking help at the Crune Museum, George discovers the tripod on the manuscript is in the museum itself, being discovered in Lochmarne, Ireland. Nico explains a professor named Peagram had an excavation in the village.
George travels to Lochmarne, Ireland and questions a man named Sean Fitzgerald about working at Peagram's dig. Fitzgerald reveals they found a hidden Templar chapel beneath the local castle ruins and Peagram entrusted a package to him, to be delivered to a 'Jacques Marquet'. Fitzgerald panics and attempts to flee, only to be run over by a Ferrari driven by a man in a pixie costume (Khan). George offers to fix the landlord's beer pumps and goes into the cellar, discovering Sean's package, a gleaming gem that Peagram discovered, identical to the one on the manuscript. Making his way inside the castle, George uses some plaster of Paris to open a secret door where he discovers a mural of a hanged man with 'Montfaucon' underneath. Meanwhile, Nico attempts to find out more about her father's involvement with Carchon. She deduces quickly that Imelda is in danger and rushes to Palais Royale to save her. Nico is too late but the dying Imelda gives Nico a key, which fits the box her father gave her. Nico opens the box and finds out the truth. Her father and Imelda were lovers and her father worked for the government as a sort of spy against Carchon's secret organization.
Back in Paris, George tracks down Jacques Marquet to the Hagenmeyer clinic. Posing as a doctor George gains access to Marquet's ward and finds him suffering from serious wounds. Marquet reveals he has hired Flap and Guido to steal the tripod from the Crune Museum. Another doctor soon intercedes and George exits. Soon, Marquet's ECG machine goes haywire, prompting security to bust open the door. They discover Marquet has been suffocated and the bogus doctor has escaped. George then asks Nico's old colleague, Andre Lobineau at the Crune Museum for his help with the manuscript. He also reveals Montfaucon is a place in Paris. George hides in an Egyptian sarcophagus until nightfall when Flap and Guido attempt to steal the tripod. George is successful in distracting them until he loses consciousness, when another unidentified thief breaks through the skylight and steals the tripod. Back at Nico's, Nico reveals she herself was the thief and gives George the tripod. George goes to Montfaucon and enters the sewers, where he discovers a secret meeting of important people including a Nobel Prize winner George met at the hotel, claiming to be the Templars. They discuss that they are looking for the Sword of Baphomet and that one of them, Klausner has gone to Syria to get a lens. George deduces that Plantard and Peagram were members of this organisation as well. The player also assumes Carchon was involved too. As they leave, George uses the tripod and gem, which splits a beam of light and lights up letters spelling 'Marib'. Nico explains Marib is a village in Syria.
George travels to Syria and discovers that Khan has already been here and asked about George and Klausner. A taxi driver named Ultar offers to drive to Bull's Head where Khan requested to go. Exploring Syria, George meets Duane and Pearl Henderson, an American couple looking for ancient souvenirs. He also deduces that the crystal ball on the manuscript is in fact the lens that Klausner was meant to obtain. George finds a statue on a stand belonging to a boy, Nejo. George sells this to Duane for $50, allowing George to pay to go to Bull's Head Hill. At the Bull's Head, George finds Klausner's corpse and takes the lens. He also discovers an idol with three bearded faces (Baphomet) and a Latin inscription describing Britain. Khan then arrives and holds George at gunpoint but George manages to escape jumping off the cliff onto Ultar's truck.
Back in Paris, Andre has deciphered part of the manuscript and it leads to the De Vasconcellos family in Spain, who were once connected with the Templars. George travels to the Villa of the family, discovering only the Countess and her gardener Lopez remain. Sneaking past Lopez, George manages to convince the Countess of his intentions and she leads him to the De Vasconcellos mausoleum, where George discovers a chessboard puzzle. Solving it opens up a panel with the De Vasconcellos chalice inside. The Countess entrusts it to George and wants him to find her missing ancestor Don Carlos.