So there's been a lot of talk lately about how to get the 3 faction ending in Fallout 4, which leaves the Minutemen, Railroad, and Brotherhood of Steel all intact and at relative peace. There's a writeup and a video floating around that outlines an incredibly complicated method of getting this...specifying things like completing certain quests before completing Reunions, and doing basically none of the BoS quests. This writeup is incredibly over complicated, and I didn't believe that any of it was necessary. So, here is how I accomplished the 3 Faction Ending. With this method you can complete the maximum number of faction quests possible, achieve the rank of Paladin and get quarters on the Prydwen, get ALL of the companion perks, avoid the issue with PAM wanting you to destroy the BOS that others have experienced, and have a Commonwealth that's at relative peace.

This is really quite simple for the most part.

Complete the Railroad quest line up to Underground Undercover. You'll fail this quest, but the Railroad won't become hostile as a result.

Complete the Institute quest line up to Mass Fusion, but don't start it.

Complete the Brotherhood of Steel quest line up to Blind Betrayal. Complete the quest, but don't talk to Maxson back at the Prydwen quite yet.

Start Mass Fusion by talking to Allie Filmore, but go inform the Brotherhood instead of relaying to Mass Fusion. This will get you Banished from the Institute, and you'll start Spoils of War. After completing and handing in Spoils of War, go talk to Desdemona and complete Burning Cover. Go talk to Preston and the quest will be complete. Avoid talking to Ronnie yet if you have Preston at the Castle, but if you do, it's not really a big deal. Fast travel back to the Prydwen and hand in Blind Betrayal. This will trigger Tactical Thinking, but don't talk to Captain Kells. Fast travel back to the Castle, and complete Defend the Castle. Completion of this quest will fail Tactical Thinking, but won't make the Brotherhood hostile. After completing Defend the Castle, just complete the Nuclear Option with the Minutemen, and you're done.

How to get all of the perks -

X6-88 becomes available as a companion after Mankind-Redefined. Getting Banished from the Institute prevents you from ever getting this perk. After completing Mankind-Redefined, take him on as a companion and max his affinity out prior to informing the Brotherhood about the Mass Fusion quest.

Danse's perk can't be received until after Blind Betrayal (as far as I know, someone correct me if this varies depending on how you end the game), so you'll be able to get this perk as well.

The Railroad remains friendly, so if you haven't gotten it yet, you'll be able to get Deacon's perk.

Optionally, if one wants Danse to remain in the Brotherhood for the end game, you'll need to complete the Brotherhood quest line up to, but not including Liberty Reprimed. This will prevent Danse from getting banished from the BOS, but will prevent you from reaching the rank of Paladin or getting quarters on the Prydwen.

I've seen a lot of people getting confused while trying to stick to the rigid order that's outlined in the unnecessarily complicated writeup that I keep seeing floating around, and it's because 90% of what's outlined in it is completely unnecessary. Hopefully someone gets some kind of use out of this. If anyone has any recommendations on variations of this to allow one to complete even more quests while still keeping 3 factions around, I'd be interested in hearing it.

I will be wanting to get this ending with one of my characters, for sure.

And, yeah, Danse's affinity can't be maxed out/his perk can't be obtained, until you spare his life in Blind Betrayal.

I would definitely strongly encourage people to do the other faction endings first. They all offer different quests that are only accessible by ending the game with them. I think this is the 'best' ending though in that it has the most quest opportunities after completing the main quest.

I vaguely recall hearing a while back that if you complete the main quest line without triggering the start of Blind Betrayal, that this requirement for maxing Danse's affinity is removed. That may have been speculation or inaccurate info though, or I could just be remembering wrong.