Now this is just an idea I thought of. I loved playing Assassin's Creed Rogue, going down a vengeful path against the brotherhood, but watching the opening of Assassin's Creed Unity where Jacques De Molay and the Templars were burned made me think of this.

Set back during the European middle ages, a young noble assassin turns to the templars, shortly before the events of Unity's prologue. Following the unjust execution of his new comrades the young knight and the other survivors travel to join with the other medieval military orders like the Hospitallers, where from within the Templars can be restored. From there the story would be about taking action with the new order and exact revenge on the pope for excommunicating the Templar knights in the first place, then travelling across Europe to bring back support as we see in many Assassin's Creed games. Following the pope the next course of action would be to take revenge on King Phillip of France and the eventually the Assassins who tipped him off, reigniting the war between Templars and Assassin's.