This is the final part of Assassin's Creed III. When it is done, you will only be able to play as Connor.
Head around the Grand Temple and make sure that you have placed all 3 of the power sources. Only with them all in place will the way be open.
Head on toward the massive door and this will trigger the next cutscene.
Continue on forward. This will bring the end of the game. Desmond makes his choice.