- "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, the newly appointed Grand Master of the Templar Order, bought Cyprus from King Richard and promptly killed Isaac Comnenus. Hearing of the purchase of the island, the Mentor of the Levantine Assassins, Altaïr Ibn-La'Ahad, visited Cyprus to rid it of the Templar threat and to find the Archive.
Quickly learning of Altaïr's presence, Bouchart sought to save the Archive's secrets by removing its contents from Cyprus. Forced to use the lives of his subordinates to buy time, he was eventually successful, and the Templars managed to relocate its contents soon 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 the Archive.
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".
In 1510, the Mentor of the Italian Assassins, Ezio Auditore da Firenze, set sail from Rome intending on sailing to Masyaf to find Altaïr's library. He used Cyprus as a stop on his journey and ventured into and explored the Archive itself, indicating that it was either rebuilt or was preserved enough that it could be explored, although he found nothing of note.