The Codex Pater Intellectus (English: Codex of the Father of Understanding) was a book written by the Grand Master of the Templar Order and Sage, Jacques de Molay, detailing his knowledge regarding the First Civilization, and personal thoughts regarding the Order.
In 1307, during the attack of King Philip the Fair's forces on the Parisian Temple orchestrated by the Assassins, de Molay tasked his advisor with hiding the Codex, along with a Sword of Eden, in the vault beneath the Temple.
As the Templar entered the fortress, he witnessed the two artifacts being stolen by Master Assassin Thomas de Carneillon, and gave chase. After a brief confrontation, the advisor used the Sword's power against the Assassin, and recovered the book, placing both in the vault as instructed. However, he was grievously disabled by de Carneillon while leaving the vault.
Four centuries later, another Sage, François-Thomas Germain, discovered the vault guided by his visions of the First Civilization, and the relics hidden within. Having read de Molay's codex, he felt a connection with the former Grand Master, and decided to reform the Templar Order with de Molay's vision in mind. However, his extremist views were met with skepticism by his fellow Templars, resulting in his exile at the hand of Grand Master François de la Serre.
Despite his exile, Germain managed to gather like-minded individuals to his cause, orchestrating the assassination of de la Serre, and ultimately the French Revolution, in order to strip the upper class in France of their power, and simultaneously give it to the people of the growing middle-class, allowing the Templars to more easily control the human populace.