I am just beginning The Molecular Level. haven't progressed in it with any of the factions, and currently in good standing with all factions (except Institute) and have done all quests offered up by all three thus far.

I want to side with the Minutemen to get the three faction peace ending and still be able to do Paladin Danse's personal quest and reach max affinity with him. Is this possible? I have spent hours watching You Tube videos, reading guides, and reading the forums and the information I've found is contradictory. On my first play through I messed it up somehow.

(Edit for typo)

Yes, it's possible. Complete the Brotherhood questline up to Blind Betrayal - after you complete that quest, stop the Brotherhood questline. In the Railroad you can progress Underground Undercover, but don't do any Institute quests that pit you against a faction (so, stop at Mass Fusion).

Do I complete (turn in) Blind Betrayal to Maxon or stop before turn in?

How far can I pursue Underground Undercover?

You need to turn in Blind Betrayal, otherwise, you can't recruit Danse, but do all the RR quests first, they won't conflict with any of the other factions, since if you turn in Blind Betrayal, PAM will get locked down and you can't do anymore of the RR quests with PAM until after the ending or the BoS is destroyed. Underground Undercover can't be complete until after you become enemies with the BoS, so don't worry about it, just do it up the Mass Fusion/Spoils of War for each faction, after that stop. Blind Betrayal is the last quest you can do for the BoS.

During my MM ending, the last quests I completed for the BoS were:

* Liberty Re-Primed

* Blind Betrayal

All I had left in my log were:

Underground Undercover

Mass Fusion

I made sure I looted everything I needed from the Institute and then killed Ayo to get kicked out (Banished from the Institute).

After that, the RR quest Underground Undercover failed.

I believe I warned the BoS about the Institute's goal concerning Mass Fusion, but I can't remember whether I actually completed that quest with the BoS. I think I just went straight MM from that point.

I went and talked to Preston. He will ask you to build up the MM, by having 8 or more settlements. I had pretty much all the settlements by then.

Once that is done, the Institute will attack the Castle and you have to defend it. After that, you will receive the final quest, "The Nuclear Option". Once that is done with the help of the Minutemen, you will still be in good standing with the BoS and the RR.

Best ending in my book.

Thank you for the tips, it's been very helpful.

"Underground Undercover" in progress

"Mankind Redefined" completed

"Blind Betrayal" completed

"Operation: Ticonderoga" completed

"Mass Fusion" (Speak with Allie Filmore) started automatically at the conclusion of "Mankind Redefined". I haven't progressed it.

Not sure what to do now to kick things off. I don't want to just murder someone at the Institute to get kicked out if I don't have to.

The only way you can get kicked out at this point is to attack the synths during the Underground Undercover while they were working in the storage room, the one where you give the synths weapons. If you let the synths escape, you will fail the quest and become enemies of the Institute, if you have already completed that, then there is no other way asides from killing the scientists.

Thank you!

As others have said, do all the BoS quests until "Blind Betrayal".

Don't progress through the Railroad quests.

Then leave the Institute, best done by rejecting to join it when Shaun offers it or by getting into a heated argument with him after "Battle for Bunker Hill". If you missed these two, then you will need to kill someone in the Institute and possibly run for your life while a legion of Synths try to butcher you.

Oh, and in Minutemen's "The Nuclear Option" quest, ACTIVATE THE EVACUATION SIGNAL when you get the chance. Otherwise, the Railroad will turn hostile and you will have to kill them all.

Oh my dear, naive kids...