### WARNING: THE FOLLOWING INFORMATION INCLUDES SPOILERS REGARDING IN-GAME TROPHIES AND ACHIEVEMENTS ###
-
After carefully considering the list of trophies/achievements, as well as other available evidence, I would like to present the following theory regarding the overall storyline, and how the various factions fit in with the bigger picture.
First of all, we know that a major theme in Fallout 4 is that of the American Revolutionary War. Also, it would appear that the first faction we encounter are the Commonwealth Minutemen, with Preston Garvey being a senior member, if not the overall leader. The fact that Garvey can be taken as a companion suggests that the Minutemen are a neutral faction, and so will never be hostile towards the player. We also know from the list of achievements, as well as the setting itself and the original codename of the project, that the Institute are the key to the main storyline. The most obvious scenario incorporated into the story will therefore be an ongoing conflict in the Commonwealth between humans and synthetics, with synthetics having been originally created to serve the institute. This also opens up the possibilty of there being a large number of advanced, 'human-like' synthetics living within the populous of the Commonwealth, who will no doubt be caught up in the greater conflict.
The remaining factions that are detailed in the list of achievements are the Brotherhood of Steel and the Railroad. The BoS, as we know, are all about controlling technology and exercising authority. And so it is more than likely that they will see synthetics as being a liability and a major threat, and will therefore want to destroy or enslave them. This is backed up by the image for the "Ad Victoriam" achievement, which shows what looks to be a giant robot, similar to Liberty Prime. This will no doubt be incorporated into the BoS endgame tactics of wiping out or rounding up the synthetic army. As for the Railroad, we already know from the Replicated Man quest, as seen in Fallout 3, that their main purpose is to fight for the rights and freedom of synthetics. This will place them in direct opposition with the BoS, which again, is evidenced by the image for the "Rockets' Red Glare" achievement, which shows the BoS airship being destroyed as seen at the end of the E3 showcase.
So how does this affect the overall storyline? Well, if we look at the achievements again, we can see something of a pattern.
The initial portion of the main questline is made up of the following five quests: 1. War Never Changes 2. When Freedom Calls 3. Unlikely Valentine 4. Reunions 5. Dangerous Minds. Following this, there are two sets of three quests that appear to be alternative paths regarding the Institute. The first set involves destroying the Intitute: 1. Hunter/Hunted 2. The Molecular Level 3. The Nuclear Option. The second set involves helping the Institute: 1. Institutionalized 2. Mankind-Redefined 3. Powering Up. Both of these branches would appear to start with the protagonist being captured by the Institute, after which we would be given a choice to help or destroy them. Following these two alternative pathways, we have 'Nuclear Family', which looks like a reunion with our now aged spouse.
The three factions also have their own questlines. The Minutemen: 1. The First Step 2. Taking Independence 3. Old Guns. The Brotherhood of Steel: 1. Semper Invicta 2. Blind Betrayal 3. Ad Victoriam. The Railroad: 1. Tradecraft 2. Underground Undercover 3. Rockets' Red Glare. Given the details I have provided above, it looks like the Minutemen will support the actions of the player regardless, with their main objective being to end the conflict and bring peace to the Commonwealth. This would give us the option of joining the Minutemen, along with either the BoS or the Railroad, depending on whether we choose to fight or defend the synthetics.
What this means is that we will be given a number of possible outcomes based on which side we take during the conflict, and whether we are for or against the Institute. The main options would be as follows:
1. Join the Minutemen and the Brotherhood of Steel
2. Join the Minutemen and the Railroad
3. Join the Brotherhood of Steel only
4. Join the Railroad only
5. Join the Minutemen only
6. Do not join any factions
Once one side or the other has achieved a significant victory, we are then given the 'Sanctuary' achievement, as the region is now in a state of peace. It is unclear at this stage if the achievement will be dependent on our fighting for the winning side. Once the conflict is over, we must then choose to either:
1. Help the Institute, allowing them to regain their status as the dominant faction in the Commonwealth
2. Destroy the Institute, allowing the locals to achieve true independence
This will result in the final story related achievement, 'Prepared for the Future', due to our having decided the fate of the Commonwealth.