Rodrigo Borgia

Backstory

Rodrigo Borgia was at the the center of a conspiracy to overthrow Lorenzo de' Medici, an Italian statesman and essentially the ruler of Florence. One night in 1476 Borgia was intercepted by the assassin Giovanni Auditore da Firenze while walking through the streets of Florence with a number of his men. Borgia immediately fled, leaving his men to battle Giovanni, however while hiding around a corner he saw one of his men who had been captured by Giovanni divulging to the assassin the plot to assassinate a powerful ally of Lorenzo de' Medici, as well as Galeazzo Maria Sforza and the Duke of Milan. Giovanni attempted to thwart Borgia's plot but was too late to stop Borgia and his men.  
 
Using a ducat (a type of coin) stolen from one of the assassins of the Duke of Milan, Giovanni deduced the origin of the perpetrators of Borgia's plot and traveled to Venice to track down the killers. In Venice a coded letter from Silvio and Marco Barbarigo to Borgia was intercepted by Giovanni who had it decoded. Giovanni delivered the decoded message to a man in Rome in order to discover who was behind the plots in Florence. The letter was passed through a number of hands before finally being delivered to Borgia. After this Borgia visited Pope Sixtus IV to gain military support for his attempts to conquer Florence. 
 

Assassin's Creed II

Rodrigo Borgia was present at the trial and hanging of Giovanni Auditore da Firenze and two of his sons; Federico and Petrucio. He also later attended a meeting with the Pazzi family in San Gimignano and a meeting with the Templars in the catacombs beneath the basilica of Santa Maria Novella. Borgia was later found in Venice, plotting with Carlo Grimaldi and the Barbarigos to assassinate Giovanni Mocenigo, Doge of Venice, so that one of them could take his position. 
 
Borgia made his next appearance to claim the Piece of Eden which the Templars had uncovered in Cyprus. Looking to avenge those responsible for the death of his father and brothers by leading the life of an assassin, the son of Giovanni Auditore Da Firenze, Ezio, donned the disguise of the carrier of the Piece of Eden in an attempt to assassinate Borgia. Borgia was prepared for Ezio's assassination attempt and engaged Ezio in a fierce battle. Losing to Ezio, Borgia called in a group of guards to assist him in the fight, however at this point the Order of Assassins arrived to hold off the guards while Ezio killed him. Borgia managed to escape Ezio and left the conflict relatively unharmed. 
 
Borgia eventually managed to attain the position of Pope and took on the title of Pope Alexander VI. Looking to once again make an attempt on Borgia's life, Ezio breached the walls of the Vatican and tried to assassinate the Pope during a mass. Ezio seemingly succeeded in his assassination of Borgia but Borgia rose up and used his Piece of Eden, the Papal Staff, to strike down Ezio and everyone else in the room. Ezio used his Piece of Eden, the Apple to create four other identical versions of himself and used them to fight Borgia with. When it once again appeared Borgia had been defeated he snatched the Apple from Ezio, combining it with the Papal Staff to open the secret entrance in the Vatican to the path to the legendary vault. Ezio attempted to stop Borgia but Borgia used the Pieces of Eden to immobilize Ezio and drive a sword through him before escaping towards the vault. Ezio shortly caught up with Borgia to find him hammering on the door of the vault. Ezio challenged the Pope to a final hand-to-hand fight without weapons or ancient relics and the two began to fight. During the fight Borgia revealed that he does not believe in God or The Bible and only became Pope so that he could enter the vault, where he believes God dwells and use his Pieces of Eden to overthrow him and gain his power in an attempt to bring Italy under the rule of the Templars. Ezio defeats Borgia but spares his life, saying that killing Borgia will not bring back the family he had lost.