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Vanilla? No there is no way to do so aside from "not finishing the game".
the institute has father that will not accept you working with the railroad, BoS, or Minutemen (though to be fair, they are all interfering with institute operations, so that's somewhat forgivable)
Desdemona will refuse to worth with the BoS, and to be fair Maxson inexplicably wants the railroad destroyed so working in a peaceful solution between these two is pretty tough. but the thing that makes absolutely no sense whatsoever is that des is completely against working with the minutemen. even though she fully acknowledges that you, as the general of the minutemen have full control over them, she still thinks they will somehow turn on the RR that shoe-horned in plot choice is asinine and makes no sense at all.
the BoS, though their mission statement pretty clearly defines a need to destroy the institute's synth lab, as well as most of their other projects, but destroying the entire institute isn't necessarily necessary and the synths themselves aren't the ultimate goal so Maxson's misguided hatred for them also means his desire to destroy the railroad instead of allying with them will shatter any chance of peace.
the closest you can get to a peaceful resolution is as follows:
1. join all factions.
2. cut ties with the institute after the battle for bunker hill, before mass fusion.
3. desdemona will eventually pull you aside and ask you to choose between them or the minutemen, you can say you choose the minutemen as many times as you want and she'll leave the door open for you to change your mind but if you make the mistake of saying you're with the railroad the minutemen story just halts.
4. follow the brotherhood all the way up to blind betrayal, save danse, and then side with the minutemen from there forward.
5. destroy the institute with the minutemen, if you choose to issue an evacuation order for the civilians and tell sturges to let anyone past that asks for it, then Desdemona will later say she disagrees with your decision to side with the minutemen but won't take action against them, and invites you to continue being a mindless peon for the railroad.
6. Preston will ask what to do about the BoS, you can choose to leave them to their own devices and not antagonize them, or to destroy the prydwen, naturally the peaceful choice has them continuing to sacrifice an endless supply of vertibirds in exchange for whateve they can pilfer from the commonwealth.
so while the BoS, Railroad, and minutemen all still hate eachother, they will stick to themselves. they won't help eachother, but they won't go out of their way to help eachother either. that's about the best you can get.
far harbor has a much better set of endings that actually makes some degree of sense given the motivations and beliefs of each faction there. in the main game, there's a lot to be desired.
Plus if you're going the bos round, The Soul survivor uses a Bos holotape to hack the institute's systems and download their files, so the bos ends up with the institute's schematics and research anyways.
There is no real reason to keep the institute around once it's assaulted. It has a serious energy issue with a reactor that's overstressed, It was designed with the idea of only having a few groups of people, it's cramped, And without the institute scientists there is nobody around to maintain it. Not only that, but once it's discovered the institute is just a vulnerable cuccoon 20 feet below ground. It's not a good position.
Best case scenario for the commonwealth is the institute/railroad being wiped out by the bos, who train the minutemen to protect the commonwealth so the bos can head home to the capital wasteland.
But in the end the game vanilla-wise cannot support all four factions working together because Reasons.
You wouldn't want to either, The institute's main defense is that nobody knows where it is. Now that everyone does, It's an extremely vulnerable hole in the ground.
The Institute needs to be nuked by the BoS more so than any faction. In fact Maxson (uniquely) should forbid evacuation. Not so much for individual G3s - we see that the BoS is rightly not too concerned with those - but to prevent scientists or others escaping with knowledge or data, schematics etc.
I did and couldn't continue the story xd
I had enough of all of them and their sht so i killed them . But then i loaded an previous save from where everyone is still alive to come in this discussion and see if i can help them all
Thank you all for your help and taking the time to reply to my question have a damn good day everyone !
Since the BOS has no intention of leaving behind a contingent once they've stripped the commonwealth bare, destroying the institute in its entirety is just a scorched earth campaign. despite the fact that the BoS doesn't want it, and would pose no immediate threat, they still don't want anyone else to enjoy that level of safety.