I'm on my second playthrough. I sided with the BoS the first time and I know I missed a lot of stuff. I'm at the point now where I've just completed "the Molecular Level" and have access to the Institute.

My goal this time around is to use the MM ending, eliminating both the Institute and the BoS. But I want to do every quest I possibly can leading up to that. I know that I'll be coming to a point now where some quests are going to be mutually exclusive. Does anyone have a list of decision points for each faction? Which quest on each path I should stop at to get the ending I'm after? Thanks!

The minute men do not kill the BoS, the Railroad does.

If the Survivor has somehow made an enemy with the BoS (through Mass Fusion or killing a named character), then the Minutemen will end up killing the BoS.

So then it sounds like I do the BoS tree down as far as Blind Betrayal, the RR through Underground Undercover, side with the Institute for Mass Fusion then get kicked out of the Institute and sic my Minutemen on them and the Bos.

Sound about right?

Sounds about right. That should end up with everyone but the RR and the MM hacked off at you.

If you do it right, you can end with the RR wiped out, the BoS shot down, and the Institute nuked. The 'kill 'em all' ending.

BoS: Tactical Thinking will make you an enemy of the Railroad, Spoils of War makes you an enemy of the Institute

Raliroad: Precipe of War will make you an enemy of the BoS, The Nuclear Option (?) makes you an enemy of the Institute

Institute: Mass Fusion will make you an enemy of the BoS, Pinned might make you an enemy of the Minutemen if you fail to convince them to stand down and you side with the Institute (I think), End of the Line makes you an enemy of the Railroad

Minutemen: Banished from the Institute will make you an enemy of the Institute