- "The Templar Archive. That's where we keep our undergarments."
- ―Maria Thorpe joking with Altaïr, 1191.[src]
Until 1191, the Templar Archive was a well-kept secret, guarded by the Templar Emperor of Cyprus, Isaac Comnenus. However, in 1191, Comnenus went to war with King Richard I of England, who swiftly defeated him and conquered the island.
Alarmed at this threat to the Archive's secrecy, Armand Bouchart, de facto Grand Master of the Templars, bought Cyprus from King Richard and promptly imprisoned and executed Isaac Comnenus. After learning of the purchase of the island, Altaïr Ibn-La'Ahad, Mentor of the Levantine Assassins, journeyed to Cyprus to thwart the Templars' plans and influence on it, though his main purpose was to obtain the information of the Archive's location in order to put a stop to Templars' access to knowledge and artifacts of the First Civilization.
Quickly learning of Altaïr's presence in Limassol, a Cypriot city where the Archive was located, Bouchart sought to save the Archive's secrets by removing its contents from Cyprus. To do so, he planned a trip to another city, Kyrenia, as he knew Altaïr would trail him. Furthermore, the content of the Archive was put into ships at the Limassol harbor, with two objectives: removing the content from the Archive, and misleading Altaïr who would think the cargo would go into the Archive. Bouchart deceived Altaïr in Kyrenia to buy time, indirectly serving his subordinates located in Kyrenia up to the Assassin. He ultimately succeeded, and the Templars managed to relocate the Archive's contents shortly before it was discovered by Altaïr. Bouchart remained in the Archive after it was emptied, and battled Altaïr and a disaffected English Templar, Maria Thorpe, when they arrived, but was slain in battle with Altaïr. Shortly after Altaïr's triumph over Bouchart, the Templars began to destroy the empty Archive with artillery fire. The complex soon began to collapse, although Altaïr and Maria were able to escape in time.
In 1228, Altaïr received word that the Templars had retaken the Archive, as Abbas Sofian, who usurped power over the Levantine Assassins, had refused to send reinforcements to defend it. Altaïr described the takeover as a massacre.
The Archive was utilized again by the Templars in 1481, when Ottoman Prince Cem used it to house an Apple of Eden, after having concluded that the artifact refused to help him in achieving his goals.
In 1510, Ezio Auditore da Firenze, Mentor of the Italian Assassins, set sail from Rome intending on finding Altaïr's library, hidden beneath the fortress of Masyaf. He used Cyprus as a stop on his journey, and ventured into the Archive itself, indicating that it was either rebuilt or was preserved enough that it could be explored, although he found nothing of note.