Far Cry 4’s main story campaign is similar to most open world ones, where you are doing missions one by one until the end. However, there are certain points within the story where you will be forced to make a decision, which is called Balance of Power missions.
Basically, you will have to choose between doing a mission for Sabal or a mission for Amita, which will be labeled with a (S) or (A) in the mission name. Picking one will lock you out of doing another, as well as create new objectives in missions following that one. The one you have chosen will lead the Golden Path until the next Balance of Power mission comes.