What is the last quest that I can complete for each faction?
For the four factions (the Institute, the Brotherhood of Steel, the Minutemen, and the Railroad), what is the last quest that I can complete for each faction, in each of their quest lines?
I completed “The Molecular Level” and got help from the Railroad, so they want me to help synths escape. And I’m also doing quests for the Institute right now.
I also want to continue quests for the Minutemen and the Brotherhood of Steel, but I haven’t received any quests from them in a while. Am I already done with the quest lines for those two factions? If I had gotten help from either of these factions instead, then would their quest lines be the ones that I would be continuing, rather than the one for the Railroad?
Is there a way for me to still continue the quest lines for those other factions? For instance, could I return the to the Brotherhood and return the Institute holotape to someone, to start a new quest? Or would that not do anything if I didn’t already have an existing quest for the Brotherhood?
I have not yet received a warning stating that I am about to damage my reputation with another faction. Also, I ultimately want to end the game as an ally of the Institute, if that matters.
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The Molecular Level quest both is and isn’t a point of no return, fundamentally it requires you to make a choice – what you do need to consider is that speaking to a faction will provide you the infiltration quest for the Institute but also make the equivalent quest for the other factions unavailable. It is possible to reconnect with the factions you didn’t choose after completing Institutionalized though.
The game is seemingly inconsistent in warning you when you’re about to make permanent changes to your faction reputations. The actual point of no return varies by faction alignment.
In the case of the Institute quest line, speaking to Allie to start the Mass Fusion quest will pop up a nice warning stating you’re about to become permanently hostile to the Brotherhood of Steel. There isn’t a subsequent warning when you do the same to the Railroad, you’ll just get lots of failed quest spam if you’ve got quests outstanding but in fairness, the mission is specifically to kill the Railroad so…
For the Railroad, I believe the switch occurs silently at the start of the quest Precipice of War. I definitely didn’t receive a message and the conversation to start Precipice of War seemed to flow continually from the conversation that ended Operation Ticonderoga – the Brotherhood of Steel just stormed in and then I got lots of quest failure spam.
For the Brotherhood of Steel, the mission that makes you hostile with the Railroad is Tactical Thinking.
As the institute what makes you hostile to the railroad, is 1: If you make the teleporter with the Brotherhood (maybe the Minutemen) when you teleport to the Institute while you have not yet completed “The road to freedom” the Railroad will no longer be your ally and you will fail the quest “The road to freedom” You will become HOSTILE with the railroad in the quest “End of the line” when you kill Desdemona (duhh…). And you will become hostile to the Brotherhood when (for me, at least) when you teleport to Mass fusion. The game will be nice to you here though, because it will give you a heads up saying “Are you sure you wish to relay to Mass Fusion, doing so will make you permanently hostile with the Brotherhood of steel”. I finished the whole main storyline with the Institute and never became hostile with the minutemen. So, if you want to come out with the Institute and the minutemen, follow the Institute, you will still be able to do all the Minutemen quests.
There is a way to finish with just the minutemen I think:
Side with the institute to kill the Railroad, and straight after that, go and murder a named institute scientist or father, to become banished (make sure to finish all possible institute side quests and collect gear first), then do the brotherhood quest up to where it’s time to destroy the institute. Then, kill elder maxson and leg it as fast as you can (save, because this may take a few tries) and follow the minutemen quests and do ‘The Nuclear Option (Minutemen)’ to destroy the institute, and after the endgame, build large artillery settlements and do ‘with our Powers combined’ and ‘defend the castle’. Make sure to have completed all side quests for each faction before doing this, as there are very good exclusives you can acquire.
There you have it. The Commonwealth with only the Minitemen left, building more shacks relentlessly and wiping out the rest of the factions.