An abbot there identified Ezio's as the monk Stefano da Bagnone's killer, and fled. He was intercepted and, once convinced that he was not about to die, the monk gave Ezio the name of the nine fingered monk: Girolamo Savonarola.[note 1] 
Journey in Spain
- Ezio: "Do you know who betrayed us to the Inquisitors?"
- Raphael: "Not yet, but we know the name of the Inquisitor Prosecutor responsible for their arrests."
- ―Ezio and Raphael discussing their situation[src]
While trying to locate Savonarola, Ezio continued to accomplish missions for the Brotherhood. Between 1488 and 1491, he went to Florence to recruit in the Brotherhood the Ghost of Florence Girolamo da Lucca, who accept the offer. Ezio also became a close friend with the Roman Assassin Lucas Bellini. 
In 1491, Ezio was told by an acquaintance to meet Antonio at the Thieves Guild in Venice. Upon arriving there, Ezio found Antonio accompanied by another man, Luis de Santángel. Luis was looking for a good "killer" who could oversee a meeting involving Luis' friend Christopher Columbus, but Ezio expressed no interest.
However, when Ezio heard that Rodrigo Borgia was also involved in the meeting, he rushed to Columbus' location, finding out that it was a trap. However, he managed to save Columbus, who explained that Rodrigo was interested in his plans to sail west. Soon afterwards, Ezio met with Antonio again, who told him to go see both Luis and Columbus in the gardens district.
They then told him that the Templars were in possession of Columbus' atlas, which featured the journey's route. Ezio quickly recovered the atlas and brought it back to Columbus and Luis. Luis informed Ezio of the presence of Spanish Assassins, who were held captive by the Spanish Inquisitor General, Tomás de Torquemada. Feeling it was his duty to rescue them, Ezio temporarily diverged from his goal to reclaim the Apple of Eden and set out to Spain, but not before Antonio gave him the names of two of his contacts. Ezio left Italy with other Assassins as Girolamo and Lucas to help their Spanish brothers.
After arriving in Spain and briefly losing his sword to a thief, Ezio met with Antonio's contacts, and was directed to the local Thieves Guild. When he arrived there, however, he found that it was empty, only to be ambushed by the Inquisitors' men.
After making his escape through the sewers, Ezio met Raphael Sánchez, who revealed himself to be an Assassin. Raphael informed Ezio of the location of the first captured Assassin, and Ezio rushed to save him. Right before the Assassin could be burned by the Inquisitors, Ezio killed all the guards and freed him.
After Ezio's return, Raphael revealed that it was Gaspar Martínez who had been ordered to capture the Assassins by Torquemada. Ezio located Gaspar and found him, Torquemada, and a guard surrounding a captured Assassin.
Torquemada revealed to the captured Assassin - and indirectly to Ezio - that Rodrigo Borgia had ordered him to capture Assassins in Spain, because they were "non-believers". After the guard killed the Assassin, the group disbanded, and Gaspar was left unguarded.
Ezio then met with him and asked him what he knew of the Templars, but Gaspar feigned ignorance and said that they "went away two centuries ago". He fell silently to Ezio's blade, and Ezio acquired a list of names of six other captured Assassins. After freeing the first man on the list, Ezio took him back to Raphael, and informed the latter of the existence of the list. However, all the remaining Assassins were located in Zaragoza.
Once in Zaragoza, Raphael told Ezio to find the Inquisition's Calficador, Pedro Llorente, whose tribunal met at the far side of town. Arriving there, Ezio found that Torquemada was also present. One of the Assassins was being tried, and after he refused to convert and confess, he was killed.
Ezio eavesdropped on the ensuing conversation, and hurried to locate the remaining five Assassins. Four of them were held captive inside some catacombs, with the last held inside a church. After securing their safety, Ezio killed Pedro Llorente.
Returning to Raphael, Ezio requested if he could return to Italy. However, Raphael still needed some help against the Inquisitors in Granada. Ezio complied, helping to assassinate a Templar spy in the city, and discovering along the way that Luis Santangel was also an Assassin.
Once again, Ezio planned to return to Italy, but was disturbed by the Templars. He was forced to fight off the Templars to defend Luis, and was informed that Raphael had been captured.
Ezio fought to rescue Raphael, and proceeded to infiltrate Torquemada's fortress. After a brief conversation between Ezio and Torquemada, Torquemada closed the gates in front of him, preventing Ezio from assassinating him.
Ezio returned to Raphael and Luis, and said that he did not believe Torquemada was a Templar himself, but only blindly followed Rodrigo Borgia's false preaching. Ezio ultimately left for Italy to resume his quest to recover the Apple of Eden, and told Luis and Raphael to inform him of Columbus' journey to find the New World should he return.
Bonfire of the Vanities
- "There is no book or teacher to give you the answers, to show you the way. Choose your own way! Do not follow me, or anyone else."
- ―Ezio after Savonarola's death.[src]
Having returned from Spain, Ezio immediately continued his quest to find the Apple of Eden. He returned to his hometown of Florence in 1494, and bumped into a monk who was running from Borgia guards, saying they were asking about "apples".