AntonioBarbarian
First time out of the vault
I'd suggest a barter solution, too. Maybe even something along the lines of making a proper feud, with people giving tribute for protection and other works. Of course, that would involve convincing both parts of the conflict.I've actually though of something now too.
So, after deactivating the bomb and moving into the town, Simms asks if you want to do another quest. The quest involves going into Springvale and dealing with the raiders, when you got the school, instead of being all hostile, the raiders in the outside would be friendly, also there would be 2 to 3 raiders in front of the main entrance plus their leader, you would have a conversation with him, which would make the quest solveable trough 3 ways. First, you would say something along the lines of "I'm sure we are all tired of talking, let's finish this now." to wich the raider leader would reply "Alright, time you meet end!" , which would make all the raiders hostile, forcing you to kill them all (both inside the building and outside). Then, the second way, by passing a speech check (around 40 speech would give around 60 to 70% of suceding, it would make the raiders stop raiding Megaton and move somewhere else. The third way would be the hardest, you would not only convince the raiders to stop raiding Megaton, but also make them protect it and Springvale (more on it later), but it would require quite the abilities, around 50 to 60 in speech to get the same 60 to 70% chance of sucess.
What bout this for the 3rd solution: Talk to raider leader, pass speech and then a barter check, he gives you one day to convince Simms of letting the raiders in and protect the town, pass a speech check with Simms, he tells you to talk to the other residents (named) and convince them, most won't care when you talk to them, Moriarty, Cromwell, Manya and Billy have to be convinced (trough a speech check with Cromwell, Manya and Billy and both a barter and a speech check with Moriarty).
Also, I though about a post-BS story, which involves essentially rebuilding the Wasteland.
After "Who dares wins" you will do a few scouting missions with the Lyons' Pride in DC, to contain the Super Mutants, then Tristan will give the Pride a quest to go into Vault 87 and blow it up, but you can ask him you could do it other way, this way would involve finding and convince both Fawkes and Uncle Leo to pacify the Super Mutants, it would need high speech, charisma and inteligence (there would be checks with both of them), after you pass these checks with Fawkes and Uncle Leo, wait around a week, a SM will approach you out of nowhere and tell you to go to the Vault 87 entrance (the irradiated one), on the Super Mutant outpost outside of it, you will find a few Mutants, Fawkes and Uncle Leo, they would all be friendly, Fawkes will tell you that they managed to convince the Muties to stop fightning, they would settle in Vault 87 and stop kidnapping people (except raiders, Talon Mercenaries, and people who attacks them), there will still be a few hostile Mutants around, but they won't respawn once killed, and DC would become almost empty, the Behemoths, if there are any left at this point, would still be hostile, togheter with a few Muties around them. Also, I haven't decided if Fawkes becomes unaveilable as a companion after the quest, which I belive he should as hes pretty much OP after BS ends. After this quest all the kids of LL move to Big Town to give space to the Muties (Fawkes will tell you he had to do it because there where too many Mutants for the Vault), and caravans stop in LL (which will have a few Muties outside to take care of the Brahmin and trade), there will also be named Super Mutants inside both the Vault and the caves which will trade with the player.
After that you return to the Citadel and talk to Elder Lyons and Tristan, making the Brotherhood "friendly" towards the Mutants and stop attacking them (unless they meet hostile Mutants).
Then you return to Megaton where you find Susie Mack and a few other Vault 101 Dwellers, she will tell you Simms wants to see you in his house and give you the key to it, when you go inside you see Simms and Amata talking, you talk to them and discover that they broke a deal, the Vault inhabitants will move to Megaton and Springvale to help them grow, and the Vaults reactor would be used to power up the town, but they demanded that Megaton be rebuilt to be a better and more confortable town, Simms will give you a quest, find a GECK, he tells you a merchant told him about the Burkittsville Vault, but they couldn't know if theres a GECK, then you can either go directly to it (Don't know how to implement it, maybe use the "Eastern Wasteland Project" http://www.nexusmods.com/fallout3/mods/16183/? as the world for it?) or go to Vault-Tec HQ in DC, go into a new area (the Basement) and repair the computer cables (you only see the DC Vaults in the mainframe because the cables of the computers with the location and data about Vaults from other areas were damaged) then acessing the mainframe and getting it's location (it would be Vault 100), once you got there, outside of it would be the cannibals, after you killed them and opened the Vault, an inhabitant (with an Armored suit) appears and talks to you, telling there was a civil war in the Vault (the experiment would that half of the population would be patriots, and the other half know communist supporters, seen what would be the effect of having two camps of different ideology in an enclosed space, and see if they would either agree to disagree and try to survive or fight until the one the sides is dead, the latter happened) and that he is the only survivor, he also asks if he can join you (he becomes your companion, otherwise you can tell him about the CW and he moves either to Megaton or Rivet City, or somewhere in the World Map where the Vault is), he also tells you about the GECK and that there are a few robots guarding it, after you defeat the robots, you get the GECK and return to Megaton, then you talk to Simms, he evacuates every one from town while you activate it in front of the Bomb, you are knocked unconsious by the blast and awakes 8 months later, in the new Megaton Clinic, still headed by Doc Church, with Andy helping him, theebuilt, like the rest of the town (I imagined Shady Sands-styled buildings), you also meet Head Paladin Tristan, he tells you that Elder Lyons is diying and he wants to talk to you before going away.
When you get to the Citadel you find him in his quarters, sitting in a couch (or something else), he tells you he fell ill in the last few months and feels hes passing away, he also tells he asked Sarah if she was ready to become Elder, to which she said she wasn't, you now must go to Fort Independence and convince Casdin to stop bickering and become Elder, but he must promise he will still aid the Wasteland, you are also given a holotape to Casdin to explain the situation (recorded by Lyons). Once at Fort Independence you must pass a very hard speech check to convince Casdin that must become Elder but still help the Wasteland, passing the check Casdin and you head to the Citadel, he talks to Lyons and accept the offer to become Elder, keep running Project Purity and helping the wastes. After the conversation the wish goodbye to each other and Lyons passes away, you then leave the Citadel and return 24 hoours later, Lyons body is cramated alredy (and disappears from the game, you can still loot him after he dies), when you return Casdin is now Elder Casdin, the Outcasts are members of the Brotherhood again (which now ocupies Fort Independence and the Outcast Outpost, which is renamed to "Anchorage Simulator", and also patrols the Capital Wasteland), though the Aqua Pura is now paid (1 cap, 1 bottle).
Thats it for now.