By 1491, members of both the Assassin and Templar Orders had infiltrated Ferdinand and Isabella's close circle in an an attempt to obtain influence over the royal house; Ferdinand's own treasurer, Raphael Sanchez, was a member of the Spanish Assassin Brotherhood.
The following year, Ferdinand and his wife bore witness to the public execution of heretics, during which the Spanish Mentor Benedicto was burned at the stake by Tomás de Torquemada. However, the two other Assassins, Aguilar de Nerha and Maria, managed to escape their predicament, leading Ferdinand and his wife to quickly flee the scene.
In 1504, Ferdinand and Isabella made an arrangement with Pope Julius II to have Cesare Borgia locked up inside the Castillo de la Mota near Valencia. Unbeknownst to both Ferdinand and Isabella, the Assassins had secretly been poisoning Isabella for having served the Borgia, thus finishing the work of her Jewish finance minister and secret Assassin Luis de Santángel. Isabella subsequently died in November 1504.
In 1507, Ferdinand waged war with John III of Navarre to conquer the lands of Navarre. During the Siege of Viana, John III gave command over his forces to his brother-in-law Cesare Borgia, who had escaped from the Castillo de la Mota in the previous year. Ezio Auditore da Firenze, the Mentor of the Italian Assassins, killed Cesare Borgia during the battle, greatly aiding Ferdinand's forces, although the Navarrese still won a pyrrhic victory.
When Ezio Auditore went on a journey to the Middle East in 1511, Ferdinand allowed Ezio safe passage through the southern territories of Italy that he controlled to return the favor of killing Cesare.