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 Sánchez, was a member of the Spanish Brotherhood of Assassins.
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 María, managed to escape their predicament, leading Ferdinand and his wife to quickly flee the scene.
In 1503, Ferdinand hired Bartolomeo d'Alviano to help the Spanish army defeat the French army in the Kingdom of Naples. 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. Next year, Ferdinand seized the power of the Kingdom of Naples in the name of Spain.
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, Mentor of the Italian Assassins, killed Cesare Borgia during the battle, greatly aiding Ferdinand's forces, although the Navarrese still won a pyrrhic victory.
Intending to curb the Venetian influence in northern Italy, Ferdinand joins the League of Cambrai created by Pope Julius II, that served as an anti-Venetian alliance that included Louis XII of France and the Roman Emperor Maximillian I. The League was initially a success, but the friction between Julius and Louis caused it to collapse by 1510.
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.
In 2012, Ferinand was one of many historical people included in the Glyph puzzles the late Assassin Clay Kaczmarek had left behind in the Animus as messages for his successor Desmond Miles to decipher. Desmond later did in September of that year. Desmond solved this puzzle, which was part of a set titled "Instruments of Power" where Ferdinand was excluded from the list of historical individuals revealed by Clay to have wielded a Staff of Eden. Later that year, he was also included in a mnemonic set in Abstergo Industries' Project Legacy.
- Assassin's Creed II: Discovery (first appearance)
- Assassin's Creed II (Glyph and Database entry only)
- Assassin's Creed: Brotherhood (mentioned in Database entry only)
- Assassin's Creed: Identity (mentioned in Database entry only)
- Assassin's Creed: Rebellion (mentioned only)
- Assassin's Creed: The Movie
- Assassin's Creed: The Official Movie Novelization
- Family Tree DNA - Assassin's Creed movie (archived)
- Assassin's Creed II: Discovery
- Assassin's Creed: The Movie
- Assassin's Creed II – Database: Bartolomeo d'Alviano
- Assassin's Creed: Brotherhood novel
- Assassin's Creed: Project Legacy – Contracts
- Assassin's Creed: Brotherhood – Database: Napoli
- Assassin's Creed: Identity – Database: War of the League of Cambrai
- Assassin's Creed: Revelations novel
- Assassin's Creed: Initiates – The Desmond Files
- Assassin's Creed II – Glyph #5: "Instruments of Power"
- Assassin's Creed: Project Legacy