Spoilers by the way.

So I just did Institutionalized (quite the quest by the way) and I'm trying to wrap my head around how this ties in with what factions are now available to me. Correct me if I am wrong.

So does the choice you make during Molecular Level, where you decide who to build the interceptor with, determine who you're ultimately siding with? Or does the choice come at Institutionalized where you agree to stay or choose to leave the Institute forever? From what I've gathered, agreeing to stay brings you on the path of the Railroad/Institute questline and then later on you'll have to make the choice between them.

However, choosing to leave will close you out of the Railroad/Institute questline and what you have left is the Brotherhood or Minutemen? Even if you chose not to build the Interceptor and get the From Within quest for the Brotherhood, they're still open as an option so long as you leave the Institute, correct? However, if you built the interceptor for the Brotherhood, you get the From Within quest and are then allowed to stay with the Institute with the Brotherhood questline open, correct?

Alright, so having choose to stay with the Institute (have not chosen between them and the Railroad yet, just doing both of their quest until I get to that point), I am basically locked out entirely from the Brotherhood quest? Think I understand most of it. I think.

Clear anything up for me if I'm not understanding something. I just want to know that exact point where faction questlines lock out. Do note, I'm not talking about when they go hostile.

You are not locked out from any Side yet ,Institutionalized is no locking point after that you still can choose between all 4 Factions and follow some of there Quests .

There Points of No Return im Not Sure for The Istitute but for RR its the Completion of Underground Undercover for BoS Blind Betrayal you can do some Parts of the Quests but cant Finish them.

You don't choose allies so much as you make enemies.

Doing Mass Fusion will make the Brotherhood your enemy, conversely doing Spoils of War will make the Institute your enemy. You can string the Railroad along as far as Rocket's Red Glare but after that you have to choose between them or the Institute. The Minutemen will never be your enemy, and you can always side with them, as far as I know.

Okay, so out of curiosity, how would you go about doing Brotherhood quests if you didn't build the interceptor for them?

I built the Interceptor for them and ended up siding with the institute, so I'm not entirely sure. I imagine it would just be business as usual with them if you built it with another faction. You'd just skip some of the stuff like recruiting Dr. Li

Yeah, I just looked into a bit more and I think I have a much better understanding of it all now. I have no interest in doing the Brotherhood quest with my current character so I'll just worry about it when the times comes.

However, you're right in that I can basically do all of the Railroad's quest except the Nuclear Option, which is good because after looking into it, I much prefer destroying the Brotherhood the way the Railroad do it in Rocket's Red Glare over the Institute in Airship down. So now I will be able to do all of the Railroad's and Institute's quest up until the end where I must either do Nuclear Option or End of the Line. I like this.

Thanks for the info. I now have a better understanding in how I will go about this.