How to make Fallout 3 good story-wise? Oh boy.. there's a lot that needs fixing for it to meld with a fully-developed adult mind so this can go two ways: 1) rip out Good Guy Emil's storywork and replace most of the dialogue or 2) completely overhaul Emil's storywork and still replace most of the dialogue.
For scenario 1) here's my premise: 50 years after the bombs, the Capital Wasteland is in chaos. You come from a vault of sorts that was designed to provide assistance to the surviving populace after the radiation had mostly cleared, but ironically your vault is reaching it's peak for sustainability and therefore you need to find resources to keep your people alive and able to thrive... or not. You can help or sabotage communities in the wasteland to benefit you and/or your people. You will need to find sources of water, food and nuclear fuel, and optionally scraps of tech to provide improvements to your and the communities of your choosing's operational capabilities. Eventually you uncover a plot by the remnants of the Chinese military from before the Great War to invade the American homeland after successfully devastating the American population and any resistance, theoretically. You can rally the communities you've helped, if any, with the optional assistance of the recently emerged survivors and descendants of the US government out of the Pentagon to stop the imminent invasion of the Red Chinese. You can fully assault (with Liberty Prime) or infiltrate their emerged super carrier/super submarine ship off the coast of Maryland to destroy them and their plan... or not. You can side with the Reds and help them in their invasion of the Capital Wasteland and bring communism to the USA and glory to the Chairman! If you follow the Good Karma path and the 'murica path this will lead to the reformation of the USA in D.C. with your vault at the heart of it and you being elected President if you choose.
Your actions will affect the status of these communities, outcome of the main storyline and your efficiency and any companions, characters and optional questlines you've involved yourself in.
For scenario 2): 200 years after the bombs, your vault is one of the last to get the all-clear signal. Prepping to exit the vault you and your people anticipate the world restored and the new-American people awaiting your inclusion, only it isn't. The Capital is still a wasteland, and in an effort to find out what happened your vault elects a scout to uncover the mystery as to why the capital still looks like a wasteland after two centuries. You travel the wasteland from community to community where you can improve or devastate the lives of the surviving inhabitants as you study the various mutations that have occurred from the phenomena. This eventually leads you to a great facility from before the war, a general purification complex for complete and total regulation of the ecozone's environment. Unfortunately instead of benefiting the wasteland it is keeping it from recovering and actually making it worse. This was done deliberately by the mysterious cult called the Children of Atom and after confronting them they capture and hold you as a prisoner. They discover your significance as a human being of pure, uncontaminated stock and see this as blasphemous, so they torture you for information of your origin and corrupt you in their experiments using a compound (virus?) originally purposed with regulating the D.C. habitat. You can manage to escape not long after being injected with the compound, if you don't join with the Children, and try to warn your people, but it is too late. They've been taken by the Children with the information you let slip, and you can now save them by rallying the communities you've helped, if any, and optionally enlist the emergent remnants of the Enclave against the evil cult to save your people before they are corrupted/killed and restore the recovery of the Wasteland. If you save your people, by the time you are ready to head back to the Vault, you are showing visible signs of mutation, and it is said by the Overseer that you would eventually contaminate the rest of the Vault populace... so you're a hero, and you have to leave.
Again, your actions will affect the status of these communities, outcome of the main storyline and your efficiency and any companions, characters and optional questlines you've involved yourself in.
Hopefully i was able to write summaries better than Bethesda, and feel free to do something with these if they hold merit. If not, at least i tried..
