Below you can find the main quests path that shows you how the main plot proceeds and what choices you can make. This graph shows you how your choice of faction affects the endings.
Bethesda created its game in such a way that it leads the player linearly through all of the missions up until the quest called Institutionalized. From this moment on, we need to side with one of the factions, thus ultimately deciding with whom we want to finish the main plot. Joining the Institute happens during the quest Institutionalized, but you can contact any of the other factions (the Minutemen, the Brotherhood of Steel, the Railroad) at any point in the game. The game does not punish you for joining all of the factions at once. However, when you complete quests dedicated to a specific faction, you can worsen your relations with another group so much, that you won't be able to do any more missions for them.
This page will be updated as soon as we investigate which exact quests block the ability to complete tasks for other factions.