I think after Fallout 3, the Enclave is totally gone, they were defeated in California, in their hidden Poseidon oril platform, in Chicago, in Washington DC... They are too weak, they won't survive and if they survive, they'll be defeated again.

@"Garska" i think they can united, but you are right about their weakness.

@Garska I would like to know where you got your information on the lore regarding the Enclave in Chicago. 

To the best of my knowledge and from what the Fallout wiki has told me, what has happened to the Enclave in Chicago is unknown. There is nothing to suggest that the Enclave in Chicago were defeated and are probably still somewhat operational.

@"Garska" i also want to know about where you got information about Enclave presence in Chicago
I remember only about BoS presence in Chicago (BoS war against Calculator)

@MrEggs0925 @Sentra My bad, I know that there is an Enclave base in Chicago (where ED-E was made) but we don't know if it defeated or not. My bad.

@"Garska" ED-E was made in Air Base Adams (Fallout 3: Broken Steel DLC) by Whitley, he asked ED-E go to one of the Enclave OUTPOSTS in Chicago, and ED-E's ultimate goal is was reaching Navarro to deliver Whitley message about Duraframe project.

@"Garska" many hours and cola with pizza in my playthrough of Fallout 3 an Fallout: New Vegas made me look a like geek.

@"Sentra" they were properly annihilated after fallout 3 the only ones left are a small group in new vegas in the guy in far harbor and some others maybe

@SweetWaterUKCG I doubt that the Enclave remnants in Chicago were completely destroyed.

Its hard to believe that Bethesda would just kill off an entire faction from the game without us hearing about it through any of there recent games. My gut tells me that since we didn't hear anything from the Enclave in Fallout 4, they will probably return in Fallout 5. In what form is unknown maybe like you said destroyed but unlikely.

@"Sentra" the enclave most likely won't come back after fallout 3 you can only be completely decimated so many times

@"SweetWaterUKCG" They may come back but i dont think at this point they can do anything really significant

The one thing I really want to know, and see explored in game is the Vault Tec storyline. I'm no lore buff but I have troughly explored all the vaults in FO3, FNV and FO4 and the more you learn, the more you get a feeling that these fuckers are still alive and well somewhere.

I mean, the Vaults are , pretty much, "for fun" experiment setups, and they're equipped with some of the most resiliant, high quality stuff you can find in the Wasteland, and that's for the stuff designed just to toy around with science. It stands to reason that they would have kept a secret the most advanced stuff they had and set themselves up with top of the line vaults for their high ranking members.

I even think it's possible that they're still operational and just waiting for the "good guys up top" (Minutemen, NCR, BoS, etc.) to clean up the surface and then exterminate said groups and take over the US for their own purposes, idk, seems possible.

What can you guys tell me about this stuff? I'd like to learn more about Vault Tec.

@Orth I understand what you mean, just having the gut feeling that the people responsible for the Vaults are still alive living somewhere, same feeling comes to mind with the Enclave. 

Interesting enough though not cannon in Fallout: Brotherhood of Steel Vault-Tec did have a private vault for its high ranking executives and personal to continue their research and live on after the war. It was called the "Secret Vault" and not even the Enclave was informed about it. The Vault was destroyed following the detonation of a Nuclear Warhead by the Initiate. Sadly though as I stated before this Vault or anything to do with Fallout: BOS is not considered cannon and cannot be considered apart of the official lore unless featured in other cannon Fallout games. 

Again while not officially lore according to the canceled Van Buren project the real purpose of the Vaults were to collect data that would assist the Enclave in dealing with the conditions and challenges of space travel. The Enclave would go to their Oil Rig, wait out the war and use the data to finish their plans and when you look at the Vault experiments, its not that far fetched.

If you want to learn more I have provided links to some different pages.

Secret Vault: http://fallout.wikia.com/wiki/Secret_Vault

Summary of Enclave Space Plans (Sebilis Response): https://www.reddit.com/r/AskScienceFiction/comments/393p9w/fallout_whats_the_purpose_of_the_vault_experiments/