Centering on Giovanni Auditore, the father of the game's main character, Ezio Auditore da Firenze. Giovanni is an Assassin living in 15th-century Italy during the Renaissance. A conspiracy is being plotted by one corrupt family to overthrow the powerful Medici family and destroy a unified Italy. As an Assassin, Giovanni must face this threat and bring the guilty parties to justice.

While giving chase to Sforza's assassins, Giovanni arrives in Venice where he intercepts a coded letter from the members of the conspiracy. Decoding the message becomes a task of great importance.

Unable to decode the letter, Giovanni decides to deliver the letter to Rome to unmask the ringleaders of the conspiracy. Once there, he discovers that the conspiracy is more widespread and dangerous than he thought.