The Rooftop Garden Protocol was an order given by William Miles, the Mentor of the Assassin Brotherhood, in late 2015 to all Assassin cells around the world.
The protocol effectively ensured the end of communications between the Assassins and the various new Initiates recruits around the world and ceased the usage of the Initiates' communication network. The protocol was enacted after various Assassins expressed their concerns about the professionalism of the Initiates and the risk on their safety, as their contact within Abstergo Entertainment had recently been killed.
The protocol reiterated that the Assassins' primary goal remained finding Dr. Álvaro Gramática and his laboratory and to not engage him on their own. Outside of that, the Assassins were free to choose their own targets, long as they acted in accordance with the Creed.