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You can save the Minutemen and ONE other faction.
The End.
Anything else is just stalling the continuation of those quests. The chain isn't over until only one of the three warring factions remains.
BUT... For the REAL happy ending: Choose an empty settlement. Create a supply line to it. Then build it up nice and cozy. Make lots and lots of defenses. Dismiss all the companions you find attractive to there. Also send all settlers you find attractive to live there. Maybe send a couple of ugly ones to tend to crops. Gather up all the chems and alcohol you have been collecting. Buy more if needed. Then retire. :)
There is debate as to whether it was intended to be 'the best ending' or not and it is a lot of work... but here are the steps:
The process:
Step 1: Before completing "Reunions," complete all main and both side quests (once each) for the Brotherhood of Steel recon team. Talk Brandis down from being crazy.
Step 2: Complete "Reunions" and "Dangerous Minds." (For proper completion, keep Preston at the Castle.)
Step 3:
(a) You will have received "Tradecraft" and "Shadow of Steel." DO NOT advance in either of these quests.
(b) Focus on the Minutemen as you continue down the main quest line. Use the Minutemen to gain access to the Institute.
© Get yourself banished from the Institute. You can play along and poke around for a bit first if you like, but if you do, you'll have to murder someone to get banished (might we suggest those bastards down in synth retention?). You may safely complete "Institutionalized," but do not progress any farther before getting yourself kicked out. Don't even speak to Father again after completing "Institutionalized." DO NOT complete "Synth Retention." (Give holotape to Sturges.)
Step 4:
(a) You will have received "Form Ranks" for the Minutemen. DO NOT advance this quest.
(b) DO NOT start "Defend the Castle." Don't even go to the Castle.
© Complete all quests for the Brotherhood from "Shadow of Steel" to "Show No Mercy." DO NOT complete "Show No Mercy." Don't even get on the Vertibird. Grab ALL side quests from the Brotherhood and keep them open.
Step 5: Complete "Form Ranks" and "Defend the Castle." Start "The Nuclear Option" for the Minutemen but DO NOT complete it.
Step 6: Complete all Railroad quests from "Tradecraft" to "Randolph Safehouse 6."
Step 7: Complete "The Nuclear Option."
~ original steps found by Sybsidian
There are a few things you have to watch out for, like you can't talk to P.A.M. as she has a Robot chip-on-her-shoulder and will start a war with the BOS, and if a Companion gets clipped by Friendly Fire they will shoot back and then blame YOU that YOU killed their friends... you also seem to miss out on a few Companion Perks (?) but other than that, all above ground Factions should call you their Hero (except Max, he doesn't like sharing limelight) and you can even do the Extended Quests for some of them (eg. BOS and RR).
This wiki will help understand the Factions a bit more, too:
https://fallout4.wiki.fextralife.com/Factions
GL with it
Edit 1:
a player named GRAY (Steam) made a refined path/list of Steps:
General Rundown:
1) Do all Minutemen quests
2) Do Railroad until you can't anymore
3) Do Brotherhood up to "Show No Mercy"
4) Enter the Institute by giving plans for teleporter to the Minutemen
5) Give Holotape to Minutemen
6) Check in with Brotherhood, Maxson will be disappointed you went to Minutemen instead of Brotherhood but you can go back to Sturges and get a copy of the holotape and make both factions happy with you, this unlocks more Brotherhood quests
7) Do Brotherhood up to Tactical Thinking, PAM will go into Shutdown mode but, at this point, everyone is still friendly and trying to kill each other. Stop here.
8) Go back to Railroad, say you'll join their side over the Minutemen, do their quests up to Underground Undercover, stop here
9) Go to Institute, do quests up to Bunker Hill. Right after going to Bunker Hill, immediately kill the courser. Battle will start, game will tell you to meet your son on the rooftops of CIT. Check in on Synths first, they will say they will leave as soon as you do.
10) Go to Rooftops, be honest that you let the Synths go because it was 'the right thing to do'. You will be banned from the Institute.
11) Go back to Desdemona, tell her you got kicked out of the institute and now the Railroad has no choice but to rely on the Minutemen
12) Talk to Preston, starts Defend The Castle, and just follow the Minutemen quests toward the ending from there.
Ends with every faction happy except The Institute, Danse alive and will be your companion, Deacon perfectly fine, PAM friendly with you, everything thuper.
Edit 2:
After reading it a bit more, it looks like the first set of steps might not be a 'true ending', as a Faction's "Ending" seems to be 'only repeatable Faction Missions left' (according to the game)... those steps seem to only get rid of the Institute and not really 'end' anything else.
I haven't finished trying these steps out myself, so maybe I'll try these sometime and try to remember to come back here to Update this, but these sounded like a possible 'happy endings' when I first saw them.
Maybe these aren't real 'endings'...
No need to go moving house just because the apocalypse happened; just build the place up, attract new residents for all those empty houses, and move on with your life.
Wrong. You can save Minuteman, Railroad, and BOS if you do the missions in the correct order all the way to the end
it has some secret misisons that will say thier is a conflict, and if ya notiffy them they will join the final fight too.
https://steamcommunity.com/app/377160/discussions/0/458604254453010183/
If you go for the Minuteman ending it leaves the BOS, Railroad, and Minutemen active at the end.
You know, I aint ever letting you hear the end of this one.....
There is not 'happy ending' That's a jRPG thing.