Like many great cities throughout Europe, it was a base for the Assassins during the Renaissance. Under the Spanish Inquisition, the city witnessed an attempted purge of the Spanish Brotherhood of Assassins that was foiled thanks to the efforts of Ezio Auditore da Firenze.
At the height of the Spanish Inquisition in 1491, Rodrigo Borgia, Grand Master of the Italian Templars, provided the names of the Spanish Assassins to Grand Inquisitor Tomás de Torquemada. Under the convintion that these Assassins were little more than atheists, Torquemada ordered the calificador of Zaragoza, Pedro Llorente, to arrest the six in his city to be tried for heresy.
After stopping the Inquisitors in Barcelona, the Assassins Ezio Auditore and Raphael Sánchez journeyed to Zaragoza to save the Assassins there; they had been alerted to the operation by a list of Zaragozan Assassins found on the corpse of prosecutor Gaspar Martínez.
The first of these Assassins was brought to the local tribunal, where he was interrogated by Llorente and his guards. Despite the torture, the Assassin resisted all attempts at conversion, a resilience that astounded Torquemada when he visited him. The prisoner was immediately executed, a scene that was witnessed by Ezio Auditore, who had arrived too late to save him.
Ezio then made his way through the city catacombs to save the remaining Assassins, causing Llorente to double the security on the last prisoner, who was held in his palace. However, Ezio managed to free him as well before tracking Llorente to the basilica to kill him. Upon their confrontation, Llorente revealed his ignorance of a Templar conspiracy, but Ezio assassinated him nonetheless for being responsible for the attempted purge. Soon after the assassination, Ezio and Raphael made their way to Granada to investigate Templar operations there.
Raid on the Assassins
In the aftermath of the Granada War, where the Assassins foiled a Templar plot to prolong the war to exhaust the Castilian treasury from funding the voyage of Christoffa Corombo, the bitter Templars retaliated by launching attacks on the homes of Luis de Santángel and Raphael Sánchez, two of the Assassins principally responsible for their failure. Both had been residing in Zaragoza at the time, and the Templars employed the Spanish Inquisition for this operation.
When soldiers of the Inquisition barged into the Luis's palace, their announced intention was to arrest him for heresy, but in truth, they planned to murder him on sight. To Luis's fortune, Ezio Auditore had been paying him a visit at the time and was there to save his life, killing the entire force of raiding soldiers. Knowing that Raphael must be under attack as well, he then rushed across the city to Raphael's estate, narrowly saving him from a guard captain that had cornered him.
Assassination attempt on Torquemada
Although the Assassins had formerly believed that an assassination of Torquemada would only incite more turmoil, the attempts on their lives changed their minds on their stance. They ordered Ezio to eliminate Torquemada once and for all right away, and the Assassin infiltrated the Grand Inquisitor's palace in Zaragoza for this purpose. Deep within the palace, he at last located his query, but as instructed by Raphael, he confronted him directly, seeking to goad him into revealing the extent of his connections with the Templars. Through Torquemada's response, Ezio incorrectly concluded that Torquemada as only cluelessly being manipulated by the Templars, when in reality, he was a Master Templar himself. By eschewing a stealthy assassination, Ezio also costed himself success, as Torquemada was able to enact a successful escape.