I remember seeing a mod that put in an entire questline for the Enclave Remnants.
After hooking up with Arcade Gannon as a companion, and then installing the mod, I believe he would approach you and say something like "I have something to show you". Here he would then take you to the secret Enclave base, open the door and show it to you/explain the history of the Enclave and the Remnants. Then he would ask you to do his a favor, to help him re-build the Enclave to his former strength.
So first you would go about getting all of the original Enclave members back. After this they give you a choice to formally induct you into the Enclave. Then after this you build up the Enclaves strength by recruiting new members, while people like Arcade train them back at the base.
Then after that he says that the base needs to be "re-built", because so many years of inactive use have turned it into shit-hole. So he sends you out to places like Repconn to retrieve power sources and other materials to rebuild it.
After that he states the Enclave has finally been restored, and now it is time to strike back. Except instead of being the horrible evil villains from FO 2 and 3, they actually help people of the wasteland, in their own way.
Well, eventually, the Enclave restored goes into a small war with the NCR, until at the end of the mod's main questline the NCR and Colonel Moore is forced to create a truce with the Enclave, allowing the Enclave to exist in the Wasteland without threat/fear of being destroyed/scattered again.
This mod was awesome. I remember my two favorite parts. 1) Where they send you back to the oil rig (and its all in rubble) to retrieve the plans for things like the Vertibird and Plasma weapons so they could start making them again. and 2) where you get to ride in a Vertibird, hanging out of the side door while shooting at NCR troopers around HELIOS I.
When I was reading about it on the website (they have an official website, but its been over a few years and I can't remember, if it even still exists) that the team who made it spent like 10,000 (and another like 4,000 or 3,000 they received in donations) dollars on the mod, they hired voice actors, bought smaller game engines and hired a small team of designers to make stuff like the ruined Poseidon Oil rig, and the new weapons. The team even had their own company which focused on providing free mods for games like New Vegas. I forgot what the hell it was called though.
Last time I checked, about 2 years ago, they said that the team wanted to make another mod for New Vegas, but that they needed like at least another 5,000 in donations to finish it. I wonder if they even finished it.