The story of the game shared similarities to the story of the Assassin's Creed: Brotherhood, aside from a few exceptions:
- Lucrezia and Caterina were located in Florence, as opposed to the Castel Sant'Angelo in Rome.
- Ezio was required to kill Lucrezia Borgia in order to free Caterina Sforza, instead of capturing her.
- Claudio, a member of the Thieves Guild of Rome, was captured by the Followers of Romulus.
- The leader of the Followers was Romulus himself.
Also, the Assassin could use a hook to kill guards or to grab onto a statue and drop it on top of guards from above.
- The Assassin's Creed: Brotherhood mobile game was set in 1486, instead of 1500 in the console game.
- The Followers of Romulus were mentioned as "Wolfmen".
- In the game, Ezio needed to visit different cities throughout Italy to assassinate his targets, whereas, in the console game, he remained mainly in Rome.
- Several targets were shot by giant crossbows, such as Lucrezia and Juan Borgia.