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1) Yes, if you say yes, you join their faction.
2) Yes, you will be able to go to the surface again.
3) I don't remember something that specific about fast travelling as soon as you agree, but surely shortly thereafter.
longer with spoilers (8 year old+ spoilers)
Read at own risk
1. Yes you can choose to stay or not
2. Yes you can go back to the surface but you gotta . . .
3. Talk to all the institute people. Just follow the tasks / quests and all the markers.
4. You can say no but you'll be considered an institute enemy from now on after you get out
5. You can kill Father or any named personnel and be made an enemy and fail all the institute quests currently active
6. Avoid killing the doctor in the weapons depot. The one from 3 that helped with the liberty prime project. If you go into a building and it has weapons and a shooting range you're in the right place avoid it
7. If you stay with the institute join them you can relay in and out no problem and fast travel from henceforth
8. You can join them and still join other factions. It is allowed.
You can join several / all factions but there are turning points. I don't wanna spoil the quests but also b/c i don't remember the exact quests and how exactly you can push so may wanna look up. I semi know some of the turning point of no return quests:
-I know for railroad you need to stop before their HQ gets attacked after the battle of bunker hill.
-For the Institute before you do the mass fusion quest to get the berilium agitator.
-For the BoS i think it was before you activate liberty prime.
-For minutemen it was doesn't matter since you need to make enemies of the BoS or Institute to trigger the minutemen quest to take them out.
You can just stop right as father gives you the 1st reclamation mission with X6-J9 or that courser companion. Once you do you can do all the quests for other companions and get all their perks and lvl them up or use console commands avoid all the hassle.
It is also advised to try to get as many items from each faction before you decide who to turn against. The most you can do is 3 way team up. Just attacking the institute. For this to work you gotta side with the minutemen. If you side with the railroad or the BoS you end up attacking the opposite faction (BoS attacks RR and RR blows up BoS airship). Minutemen you can just go directly for the institute either becoming an enemy by attacking them or during a castle defense synths can attack and you can get the quest directly afterwards to attack the institute.
You can also just not finish the quests and do radiant quests for each faction to lvl up or get items. Focus on settlement building or getting items. People have made save games at the time just before you gotta do the point of no return missions for each faction.
There are also mods people made for each faction. Example there is one mod that father lives, gets into a suit of PA, and becomes a companion. Another RR / Institute peace treaty but the BoS still turns hostile. There are mods that restore some cut content like Danse taking over as elder or you becoming elder of BoS and the BoS + minutemen attack on the institute. I'd save the mod playthroughs though for when you play 1 of each playthroughs so you can truly appreciate them.
A reasonable person might be forgiven for thinking that the commitments you make to the factions are binding or meaningful. Not in the Bethesda-verse. You are just playing them along. In effect the one-way 'deal' is always "ok you guys can make all of your facilities and capabilities available to me until such time as I finally get around to murdering you all". That goes for Institute, Minutemen, Brotherhood, Railroad, or even for lesser factions like Diamond City or Bunker Hill.