The search for Cesare Borgia was an event after the Liberation of Rome, in which members of the Assassin Order attempted to determine the location of Cesare's imprisonment, with the intention of assassinating him.
- "There are women in this city who may help us. We must seek them out and talk to them."
- ―Ezio revealing his plan to Machiavelli.[src]
Immediately after the imprisonment and escape of Cesare Borgia from the Castel Sant'Angelo, Cesare was sent to a different prison. His location was kept a secret and only Pope Julius II and King Ferdinand and Queen Isabella of Aragon and Castile were allowed to know of his location. Not even the Mentor of the Italian Assassins, Ezio Auditore da Firenze, was allowed to know his location.
Ezio and Machiavelli immediately started their search for the Templar Grand Master, tracking down and interrogating ex-lovers and other associates of the Borgia family. Their first destination was the house of Vannozza dei Cattanei, Cesare's mother. However, she was not able to give any new information to the Assassins, and they set off to interrogate Giulia Farnese, Rodrigo Borgia's last mistress. She too was unable to provide the Assassins with useful information. After that, Ezio and Machiavelli visited Charlotte d'Albret, Cesare's wife and the mother of one of his children. After a brief conversation, they left her to her own devices, still without a clue about Cesare's whereabouts.
- "They have a hideout in the Prati - just to the east of the Vatican. That's where they've taken her."
- ―Bruno revealing the Borgia diehards' location.[src]
While on their way back to Tiber Island, Ezio and Machiavelli discussed the use of the Apple to find Cesare, but Ezio was hesitant, wanting to rely on his own skills, and not just on the Apple. However, their discussion was soon interrupted by Bruno, one of Machiavelli's spies, who told them the Borgia diehards had captured Claudia. The Assassins made their way to the Borgia hideout, only to find themselves ambushed by the diehards. During a brief conversation, the diehards revealed that Bruno was actually working for them, and that they in turn worked for Micheletto Corella. Ezio and Machiavelli managed to fight of the diehards and free Claudia without too much trouble and quickly made their way to their hideout, deciding they would try to find Micheletto, as he would lead them to Cesare.
- La Volpe: "He’s got contingents from the Romagna towns still loyal to Cesare. He’ll put up a fight."
- Ezio: "Let him!"
- ―Ezio and La Volpe discussing the assault on Micheletto.[src]
Not long after that, La Volpe came to Ezio, telling him his spies had found Micheletto, who was hiding in Zagarolo. Immediately, Ezio gathered an army of a hundred Thieves and Apprentices, marching for Zagarolo the following morning. Micheletto and his Borgia-diehards fought fiercely, but they were no match for the Assassins' forces. Machiavelli arrested Micheletto and he was then taken to Florence and locked up in the Palazzo della Signoria.
While Micheletto was locked up in Florence, he was tortured by Machiavelli, Piero Soderini and Amerigo Vespucci, who were determined to find out where Cesare Borgia was imprisoned. Meanwhile, Ezio and Leonardo da Vinci traveled to Gaspar Torella, Cesare's personal doctor, to ask him about Cesare's whereabouts. However, both attempts proved futile. Machiavelli soon traveled back to Rome to meet Ezio. He informed Ezio of Micheletto's escape from prison. Borgia-diehards had climbed the prisons roof and lowered a rope to allow Micheletto to climb out of his window and escape. The bars in front of the window were removed with a file, which was smuggled in by the priest that took his confession. The Assassins now decided to find Micheletto and follow him to Cesare, and Ezio agreed to use the Apple to do so.
Journey to Naples
- "Where is that rocca? What is the Apple telling us?"
- ―Ezio questioning the vision from the Apple[src]
Ezio and Machiavelli turned to the Apple of Eden for help, but the only thing it showed them was the picture of a castle, somewhere in Spain. They then decided to ask Leonardo da Vinci for help, as he had studied the Apple and knew more details about it. In the second attempt to use the Apple, it told Ezio he had done well and had to ride for Naples, from where Micheletto would set sail for Valencia. The Apple also told him he would have to continue his journey without it, as it would no longer help him.
Ezio and Machiavelli traveled to the secret room located underneath the Colosseum to hide the Apple and joined Leonardo for the ride to Naples. Soon after their arrival, they met Camilla who told them Micheletto had indeed set sail for Valencia. Ezio, Machiavelli and Leonardo quickly decided to follow him and head for Valencia.
Ezio, Machiavelli and Leonardo set sail for Valencia in pursuit of Micheletto. The Apple remained safely hidden in the Vault underneath the Colosseo.