This trophy is story-related and cannot be missed via normal campaign progression.
This is the final sequence. You will have to climb the outside of the Vatican and make your way across the rooftops. You can kill the guards or run past them, your choice. When you get to the area with the monks you can blend past a couple of guards.
Once inside the Vatican, you can creep your way so you are above Rodrigo. Pounce on him and begin your fight. It takes a long time to defeat him as he apparently has a lot to say. When you wound him enough he will severely wound you and disappear.
Follow him to the vault and fight him again using only your fists. Again this fight will take a little time because Rodrigo can never shut up. Beat him a second time and enter the secret room for a butt-load of cutscenes. Your trophy will pop after a few of them.