I thought I'd come up with a concept for Fallout 4 using fanon material, twisted to my whims.
2277: thirty years after a bloody and ultimately pointless war between the Brotherhood of Steel and the New California Republic. They have spent these years rebuilding their strength in the west and now the time has come to reconnect with the distant outposts of the Brotherhood. As a Brotherhood initiate, your first mission outside of Lost Hills will be to join a squad of Brotherhood soldiers and diplomats to reassert the authority of the Western Elders. Will your travels take you to Chicago where dissenters traveled by airship? Will you go to D.C. where Paladin Lyons got a battlefield promotion for finding some mysterious super-weapon before going local? Ah nope...looks like you're going to some little place you never heard of called Fort Fritz. Prior to the loss of contact there were some rumors of unconventional activity that the Elder there needs to account for.
After a brief, totally not retarded tutorial in Lost Hills you get treated to a cinematic of a small Brotherhood caravan traveling towards New Mexico, only to be attacked by the steam chariots of Caesar's Legion. Left among the dead, you awaken to find that most of your brothers have been taken as slaves. Alone, with what meager supplies that weren't looted you must complete the trip on your own.
In Fort Fritz you find a sympathetic Elder Fritz. Without the senior members of the caravan you can't really complete your mission as you don't have the authority to demand sweet F-A from the Elder. He promises to look into the kidnapped members of the delegation and suggests you make yourself useful in the meantime. Fort Fritz relies heavily on the nearby Republic of the Permian Basin for a number of its staples and supplies, but there seems to be trouble in the region. It's not the Brotherhood's mandate to deal with those troubles per se, but Fritz doesn't think sending a lone initiate will do much harm.
The Republic territories offer a number of mini-quests of course and side stories branching between helping the Salt Clan and Rockers or their adversaries in the Republic Council. Much of their troubles have to do with the vicious Sand Hills Tribe, though there would be other diversions as well. You would also have the opportunity to perform some tasks that are clearly bad for the Republic leadership, if not the Republic itself.
Eventually, Elder Fritz informs you that the kidnapped Brotherhood members are to be sold in the town of Monahans. If you've generally acted in a pro-Republic fashion (regardless of which Republic faction), you'll be given the choice of infiltrating the raider town with some Republic commandos. If you acted in a primarily anti-Republic fashion, someone will contact you with an opportunity to purchase the Brotherhood soldiers and get revenge on the Legion. if you were neutral the whole way, Elder Fritz gives you the option of trying to infiltrate the place on your own or lead an attack with his small team of Paladins to rip the place a new one.
After the rescue, it becomes apparent to the Initiate and Elder Fritz that the Sand Hills Tribe is led by Andor and Chrysanthemum Arceneaux|former members of the Brotherhood, a pair of siblings who are willing to reconnect and submit their vast trove of scientific lore to the Brotherhood if assisted in their scheme to simultaneously destroy the tribe they themselves created while subverting the Republic leadership. Alternatively, you could attempt to apprehend the duo by force, but they weren't in Monahans, leading to a new investigation to find them.
In the end you can choose to aid the Republic (and one of the two factions within it) or subvert it (by killing leaders or helping the twins replace leaders with surgically altered minions). You also get to learn Elder Fritz's secret: he's been employing ghouls living under the fort to repair and build technology in exchange for protection, something not generally done by the Brotherhood.
The specifics of the endgame depend on your choices and character build, but possibilities include attacking the twins beneath Rattlesnake Bomber Base (which would be a trippy, freaky kind of maze ala the Master's Vault), gunning down a Republic faction in their strong point, acting as mediator/negotiator to work out something between one or more factions, etc. After the last battle or what have you. Then you get debriefed by one of the Paladins you rescued, during which time you can speak in defense of or against Elder Fritz. If you had become a Scribe earlier in the game, you'd get promoted to Head Scribe of Fort Fritz. If you elected to become a knight you would be given the opportunity to become a Paladin. Cue ending credits, then you get to freeplay the aftermath.
- Powell Stantzmann: Would turn on you if you sided with the Tribe.
- Jeremiah Claffey: Would turn on you if you sided against the Tribe.
- Alec Burton: Has a sidequest to find lost family members.