QUOTE(RaderOfTheLostArk @ Apr 8 2018, 01:00 PM)

Decided to finally go inside the Institute in Fallout 4. For roleplaying purposes, and because I was curious about looking around, I went with the "not sure" option about joining the Institute. But there is no way my character is actually joining them. I assume that with the quest "Synth Retention" that is the point where I can finally tell Father that the Institute can burn. That is where I left my character at last night.
Fallout 4 is very different from the other Beth games when it comes to the Main Quest and Faction quests. Technically the Main Quest ended the moment you stepped inside the Institute and first spoke to Father (the Institutionalized quest).
From here on out the Faction quests take over. There are four Factions: Institute, Railroad, BOS, and Minutemen.
The Minutemen are pretty much completely separate from the Institute. In fact, you can do the Minuteman questline to completion and never set foot inside the Institute.
The Institute questline is of course all about joining the Institute.
The Railroad questline requires you to pretend to join the Institute for a pretty long time, but in reality you are a spy for the Railroad working to destroy the Institute from within.
I never finished the BOS questline, but from what I gather it is a more direct and open war against the Institute, and it ends with you destroying the Institute as well..
So how you respond to Father influences what you can do with the other questlines. Telling him to F off fails the Railroad questline, since you need to be on the inside to accomplish it. It will work fine with the Minuteman questline though, and I imagine it will be ok with the BOS questline as well.