I've noticed a lot of people complaining saying that Fallout 3's story is terrible and that it ruins the RPG experience. I have thought over this and compiled a list of changes that would enhance FO3's story and make it sensible, and better to the RPG experience. Broken Steel is also abolished.
Firstly, your Dad should have instead been quite abusive like Tammy Hargrave, therefore you aren't forced to love daddy.
Before you first enter the Citadel, all crimes against the BOS are forgiven but you are not allowed any weapons or clothing inside there. Any more crimes and you are not allowed in there ever again.
The player can sometimes get dialogue options about things they know nothing about when they leave the Vault. This should be remedied by unlocking dialogue options by completing certain quests, certain items, or finding things out.
After leaving Eden's Office, Colonel Autumn confronts you. After a long conversation he asks you to join up with him. If you refuse, he is about to kill you but an explosion occurs and rubble blocks you both off, and the game carries on as normal. However if you are permanently hated by the Brotherhood, you must side with Autumn, or fight the Purifier on your own.
If you accept, Autumn asks you to hand over the Vial. However, you can try to Lie that you don't have it. From here on, the Game brings up a Box forcing you to select a decision: Brotherhood, Enclave, or Yourself. Whatever one you choose, if you attack any of that faction, the game automatically reloads a previous save.
If you choose Autumn, you follow him & his forces out of the RR. You & his entire Army get Vertibirds to the Satellite Relay Station.
Once you get there, you are asked to find Power Cells from Olney Powerworks. These Power Cells will bring the Orbital Cannon back Online again. Then, Take It Back! begins. You get a Vertibird to Andale. You then fight Brotherhood Forces over to the Tidal Basin. After Liberty Prime is destroyed, you get a raft to the Memorial. You fight against Enclave Forces Loyal to Eden, and get inside. At the Rotunda, you are confronted by Sentinel Sarah Lyons. You kill her, and Dr Li comes on the intercom thinking she is talking to Lyons. Then, you must activate the Purifier, and add the Vial if you successfully lied about having it. You will then die.
Or, if you selected Yourself (only if you are hated by the BOS as well) you will go over to Taft Tunnel and begin the quest on your own. Fight through Enclave Forces, fight through the sub-basement, the Gift Shop, and detonate mines set up by The Enclave outside the Memorial to kill them all. Then, confront Autumn in the Rotunda. You will get an intercom message from an Enclave Soldier outside telling the Soldiers to activate the Purifier warning that it will explode. Do whatever you need in the Purifier. You will then die.