|“|| "You can't!! You can't!! It's MY destiny!! MINE!!! I am the prophet!! "
Alexander VI. His enemies called him "The Spaniard", because of his Spanish origins, while his Templar followers called him "Maestro", which is Italian for master.
The Medici were the ruling family in Florence, but a conspiracy was being plotted in an attempt to overthrow the powerful Lorenzo de' Medici, and Rodrigo Borgia was at the centre of it. Rodrigo's men took down important leaders all over Italy, so they could seize control. He was the one that ordered the execution of the Auditore family, from which only Ezio, Claudia and Maria escaped. Two years later, Rodrigo attended a meeting with the Pazzi family under the Basilica of Santa Maria Novella. There he reminded them to beware of the Assassins, and stated that the next day would be "A new dawn for Florence".
After Ezio had thwarted the Templars in Florence, Rodrigo went to meet with the remaining conspirators in Tuscany. The Pazzi were going to ask for asylum in either Venice or Rome. But before the meeting could even start, most of the conspirators were killed by Ezio. Only Jacopo de' Pazzi made it to the meeting. Rodrigo blaimed him for the failure in Florence and stabbed him. He then left, after sending his men after Ezio.
Borgia was later seen in Venice, planning with Carlo Grimaldi and the Barbarigos to murder the current Doge, and replace him with a Templar. He was angry with them for making their own plans, and appointed Marco Barbarigo as the new Doge. While Ezio was hunting the Barbarigo's in Venice, Rodrigo was tracking the location of a Piece of Eden in Cyprus. He planned to use the Piece of Eden to create a new world, with himself as its leader. He appeared in Venice, claiming the Piece of Eden, but Ezio attempted to kill him, resulting in Rodrigo to flee without the Piece.
Borgia was elected Pope in 1492 and established his power in Rome. Borgia's true intent however, was just to get in the vault that lays under the Vatican, where he believed to find God.
In 1499, Ezio chased him to assassinate him. Ezio sneaked into the Vatican and seemingly assassinated Borgia without being seen inside the Sistine Chapel. After Ezio spoke to Borgia, Borgia used the Staff of Eden to strike down everyone in the room, including Ezio. Ezio later managed to resist the power of the staff, and took out the Apple of Eden. Using the Apple of Eden, Ezio created 4 clones of himself, which aided him in his fight against Rodrigo. Rodrigo beat Ezio, and managed to combine the Apple of Eden with the Staff of Eden, making him very powerful. He stabbed Ezio, leaving him for dead, and entering the Vault. After awaking a short while later, Ezio made his way into the Vault as well, and found Borgia furiously pounding the door to the inner chambers. Ezio challenged Borgia to a fight without any weapons, and he eventually won the fight. Rodrigo stated that he never believed in the Bible or in God, and only became Pope to get the Staff and access to the Vault. After beating Rodrigo, Ezio told him he was not the prophet, as Ezio was the prophet. Broken by this revelation and accepting defeat, Borgia told Ezio to kill him and put an end to it; however Ezio refused, saying that killing Borgia would not bring back his family. Besides, the knowledge that he was not the Prophet was an even sorer blow than anything else that Ezio could have thought of.
In the sequel to "Assassin's Creed II", ("Assassin's Creed: Brotherhood") Rodrigo Borgia is still the Pope, but is later killed by his son, Cesare Borgia out of rage.