Rodrigo Borgia is the Apple of Eden bearer who becomes a major antagonist in Assassin's Creed II.
Rodrigo Borgia is the Templar Grand Master known as the Spaniard. He seeks Pieces of Eden and uses political influence to advance the Templar cause. In the game's climax, he possesses an Apple of Eden and confronts Ezio at the Vatican in 1499, where Rodrigo has become Pope Alexander VI.
The game fictionalizes the historical Borgia family and blends real political events with the series' supernatural technology. Rodrigo is not the final target Ezio kills: Ezio defeats him but spares his life, leaving the later confrontation with Cesare Borgia to the 2010 follow-up, Assassin's Creed Brotherhood.
Cesare is the most likely mix-up because he is Rodrigo's son and the central antagonist of Brotherhood. Girolamo Savonarola and Francesco de' Pazzi are also historical villains or conspirators in Assassin's Creed II, but neither is the Rodrigo Borgia character who bears the Apple in the finale.