*****ENDING SPOILER WARNING BELOW*****

I put over 200+ hrs into the game before finally heading into the end game. None of the choices seemed satisfying due to having to annihilate the other factions despite the fact the faction you choose to survive is riddled with their own imperfections. Some good posts on here argued that heading up the Institute was the best possible choice because they have a lot of toys and you would be in a powerful position to make real changes to the commonwealth, perhaps even reversing some of the institute's ugly utilitarian view of sentient synths and their disdainful views of the common folk in the wasteland.

I begrudgingly went down this path despite not really liking the Institute, but the last straw was that awful broadcast Father has you help with where you announce to all the wasteland over radio that "we're back, but don't worry, the Institute has no desire to meddle in your UNIMPORTANT daily lives...". (they actually use the word UNIMPORTANT, how insulting!)

I'm glad it happened because I did a lot of research at that point, reloaded a prior save and was able to pull off the 3 faction friendly ending that I didn't even know existed! I have to say to anyone looking for a more peaceful and satisfying way to complete the game, this is the one and it has a number of benefits including:

1. You have top standing with MM, RR, and BOS and continue to receive radiant and new quests from all three of them
2. All the interesting main characters from those factions remain alive (except one scripted to die)
3. You get your own room on the Prydwen which remains aloft!
4. At least the way I did it, it completely skipped any battle using the idiotic cliched ballpark-megaphone voiced giant Liberty Prime robot. To me that is such a weak and unbelievable part of the story, I was happy to not see it in action.
5. You help most synths escape (or so says Desdemona) and further evidenced by the new radiant quests to help smuggle them
6. And you still get to nuke something, the Institute, which is perhaps the most misguided and evil faction. I would have liked to have had a nice clean underground room to call home but you can't even bring a follower there so I probably wouldn't have used it anyway.

What is not to like about it?

Rainbows 'n unicorns.

How/when did you clear university point? I don't remember exactly what I did but I got to a point where I was on good terms with the institute and all of the other factions but had done very little for the railroad, and then they gave me a mission to clear out university point.

When I got there though it was populated by just synths, which were friendly to me so I was basically unable to complete that mission for them, preventing me from moving forward in their story line.

What's the point of no return here? Building the stuff to enter the Institute?

Mass Fusion, where you have to get this special fusion core/cell. Whichever side you choose, everyone else will hate you.

there is no way there can be three surviving factions if you complete the MQ. At one point or another the factions will start wiping each other out.

Mass Fusion is done for the BoS makes you enemies of the Institute, and the other way around. If done for the Institute your instant enemies with the BoS.

in my game I played down the middle as far as I could go up to Mass Fusion. Mass Fusion made me enemies with the BoS who then later attacked the Railroad. With help of the Railroad I took out the BoS but was then tasked by Father to take out the RR... so I did. but not before the Institute wanted me to take care of the MM. Somehow I managed to spare the MM peacefully but now the RR and BoS are no more.

So the only way I can see three factions remaining is by NOT completing Mass Fusion.

That is indeed the case. The path I've plotted is to get banished from the Institute after the Battle of Bunker Hill, after which you lose both their questline and the Railroad's questline. You can keep doing Brotherhood quests up until Tactical Thinking, which makes you enemies of the Railroad. Do Defend the Castle instead, which causes Tactical Thinking to fail, and then the Institute will surely be your only enemy.

I got the big detonation, the final video ending, as well as Travis and Freedom radio announcing the Institute was destroyed.

*** WARNING MEGA SPOILER BELOW ***

This is what I did (or at least as best as I can remember). Essentially it is the Minute Man ending, chosen as late as possible in the game:

1. I did all side quests I could find for all factions. I got all the mats for Liberty Prime, synth missions, built plenty of settlements, etc...

2. I don't think the Battle of Bunkerhill matters that much. I didn't notify BOS or RR and was there on behalf of the Institute. I opened the mission by murdering the courser and then killed BOS, RR, and Inst. factions on the outside (they were all attacking settlers for some reason). I killed BOS and Institute inside, but not the RR and chose to free the synths as the final quest choice, siding that battle with the RR. I lied my way out of it with Father so did not lose status with the Institute (remarkably after murdering every single synth they sent on the mission). Subsequent to the quest, neither BOS nor RR complained about me killing their troops.

3. Did up to and including the Inside Job quest line. You need something from the Institute that you get on this quest to complete the MM ending, so I think it has to be gotten before you fall foul of the Institute, are banished and can't teleport back in (but not sure there isn't another way).

4. This is a critical part. The last step of Blind Betrayal is to talk to Maxson, get your Paladin status and your room aboard the Prydwen. I don't think dialog options here are that important. But at the conclusion of the conversation Tactical Reasoning is started and you are ordered to talk to officer Kells. *** DO NOT GO NEAR KELLS OR OTHERWISE TALK TO HIM !!! *** He will aggressively grab you into a dialog which I don't believe has an option to get out of without accepting the mission to kill Desdemona and rest of the RR gang. It gives you enemy status with the RR upon finishing the conversation, so it's critical to avoid him. This quest is not required. It will auto-fail in the MM ending quest line with no negative affects to your BOS status. And you will be off the hook to kill Desdemona and the RR characters!

5. On Mass Fusion I chose to tell the BOS and retrieve the Beryllium Agitator for them. I didn't finish Mass Fusion immediately as I did step 6 (below) first but not sure it matters.

6. Upon notifying BOS in Mass Fusion, you are immediately put into enemy status with the Institute, starting Banished From The Institute. You'll get a quest choice to tell Desdemona, who will direct you to get help from your own Minute Men, opening up that quest-line ending.

7. I finished up Mass Fusion for BOS, but then did nothing else for them other than some "technical documents" and the blood thing.

8. Finished the game with the Minute Men ending quest line.

Post ending, in terms of dialog, the BOS all complain about using the MM instead of them but they are positive about the prospects and congratulate you on your victory. No BOS status change. The MM are all beaming with pride. The RR is happy and congratulates you. PAM resumes her radiant quests (which she seems to bug out and stop giving after Tactical Reasoning starts). So this leads me to believe this is a legit written in ending and not one gotten through exploitation.

***SPOILERS AHOY***

Yeap, 3 factions ending for me too, the Institute has nothing to offer after all: the store is worth nothing, the radiant quests are glitchy as hell and the institute are like Mengele, but too busy to care. You do get synth equipment nonetheless from the PAM missions even when Inst is obliterated.

I concur to TravisBickle's post, you get up to the Mass Fusion mission for Inst and Underground Undercover for RR (up to giving a password or talking to a synth, beyond that you might get hostile with BoS).

I got my bad rep with Inst whilst inside: by VATSing Father with my Gauss Rifle. I got Banished from Inst and talked with Preston for Defend the Castle and Desdemona for her plead to do something with the Minutemen since they lost their edge. Then I went and did everything BoS up until the Captain Kell mission (very important!). Then went on with Minutemen and, presto, you get everyone worthwhile in the Commonwealth siding with you.

You get lil Shaun with his Wazer Wifle, you get Tinker Tom and Teagan stores, you get new missions with nice xp and some neat new equipment.

Some notable points before going bananas in th Institute and then: Get the X6 perk (it sticks with you even when you get hostile), get the unique equipment from the synth store, do as many missions as possible (like the seeds one) and get the FEV stuff done for Virgil. Also, before you nuke it, send the evacuation message, I think it is essential for a RR radiant mission endgame.

Excellent points especially the evac message! I think if you don't give that, the RR becomes hostile. For once a dialog choice matters.

I didn't think ahead on the X6 perk and unique weapons, so I guess that is next play through or perhaps some console codes. Maybe I can resurrect the synth companion and addtofaction ...

I'm on my second play through currently, and I'm considering doing this ending. I'm still fairly early in this play through, so I've got plenty of time to decide.

I've read all about it so I know how to get it and everything...but honestly I think this is the worst possible ending to do for the first play through. You are missing out on SO MANY awesome quests by going this route. I made a hard save prior to the point of no return (Mass Fusion/Spoils of War) so I could complete all the endings. I did it with the Brotherhood of Steel first, then went back to this save and did the Institute, the Railroad, and the Minutemen (not the 3 faction Minutemen ending). Some of these end game quests are among the absolute best in the game. By going right for the three faction quest, you're seriously missing out on at least a third of the quests in the game.

I would strongly recommend doing the other endings at some point. I may do it for this play through just to leave more options for radiant quests after finishing it, but I haven't decided yet.

Yeah I didn't account very exhaustively through what I might have missed. I did follow the Institute, RR, and BOS paths, post Mass Fusion, each to some extent but ultimately came back and reloaded a prior save to the Mass Fusion point. I destroyed the Prydwen a couple times, but I didn't see Liberty Prime in action (although don't feel I missed much). But that is a good point, I might want to at least reload some saves and explore the other endings (as hard as it might be to murder all the characters I like).

Well, you do get all the other quests done with prior saves for the trophies, so you get to see them, then you go to the no return point save and go ahead with what I consider the proper ending. At games like this I can't get myself to doing multiple playthroughs, I want to max out that one playthrough (I am currently lvl 103).