This page contains a summary of Fallout 3's plot.
Escaping Vault 101
You, the Lone Wanderer, are a young inhabitant of Vault 101. The Vault has supposedly been sealed for the last 200 years, with nobody entering or leaving it. All was going well until your father, James disappeared from the vault without any explanation. During the ensuing commotion, you also escape the vault and set off in search of your father.
Rust, decay, and creeping vegetation infest monuments from before the Great War. Amidst the ruins of Washington, D.C., the Capitol, the Jefferson Memorial and the battered remains of the Washington Monument still stand in the desolate area that is now known as the Capital Wasteland. The central hub of civilization in the ruins of the former capital is Rivet City, based in the remains of an aircraft carrier carried far inland and beached by a catastrophic tsunami whose waters have long since receded. Other settlements include the towns of Megaton, Arefu, Tenpenny Tower and Paradise Falls. Movement through the downtown area and settlements is possible through the Washington Metro tunnels and crossing the desolate nuclear wasteland.
The Brotherhood of Steel community is stationed in the Citadel, built in the ruins of the pre-War Pentagon where they attempt to preserve as much pre-war technology as possible. Super mutants, who since emerging from their refuges, have waged an unceasing war against what remains of humanity, trying to invade their territory and capture them.  The Enclave - the self-styled inheritors of the power of the United States government - under the leadership of their new President John Henry Eden and his ruthless second-in-command Colonel Augustus Autumn, are the player's biggest foes in the game.
As you search for your father, either through Three Dog, DJ of Galaxy News Radio, or by speaking directly to Madison Li in Rivet City, you learn that he went to the now abandoned Project Purity site located in The Jefferson Memorial. His, and the other scientist's aim was to complete Project Purity, and purify huge amounts of water for the entire wasteland. However, when you reach the Jefferson Memorial you find a holotape detailing his search for the brilliant Scientist Doctor Stanislaus Braun who worked for Vault-Tec before The Great War and now resides in Vault 112. Upon finding and entering Vault 112, you find that all the inhabitants have gone into virtual reality simulators, where they have remained since the bombs fell.
After entering a stasis pod and loading the Tranquility Lane simulation, you find yourself in a picture perfect, pre-war town. You talk to Betty, Dr. Braun's alter-ego within the simulation, who asks you to do cruel and sick "pranks" on the people of Tranquility Lane. Upon doing so she begins to speak with a startlingly male voice and allows you to ask a single question which she will answer to the best of her ability. Eventually she tells you to kill everyone in the simulation.
Alternatively, you can use a fail-safe computer terminal in the abandoned house to override the simulation. On the computer are the records of how Stanislaus Braun has been playing cruel games with the residents of the Vault, sadistically torturing them and then changing the simulation when it got "boring." Also, on the computer is a fail-safe program that initiates a simulation of a Chinese invasion (borrowed from the government at his request), which deactivates a "safety protocol" and physically kills the residents of the vault. However, Braun cannot deactivate his own safety and therefore cannot commit suicide, leaving him alone with no one else to torture if you choose this course of action. After completing one, or both these paths, Betty reveals that your father has been inside the simulation as the dog near him, Doc. You are then free to leave by a door that materializes next to him.
After exiting the simulation, your father then emerges out of a stasis pod and tells you that he went to Braun because he wanted to confirm that the G.E.C.K could be used for Project Purity.
Once your father is free, he asks you to help him reinitialize Project Purity. He travels to Rivet City to find Dr. Li and the other scientists that formerly worked on the project with him. After some arguing, he convinces them to resume work on the project. Once he does, you go to Project Purity's headquarters and help make several repairs, after which you are attacked by the Enclave.
Upon your return to the control room you find your father locked inside the control booth talking to Enclave Colonel Augustus Autumn who states that the Enclave is taking over Project Purity. Your father then floods the control booth with radiation, sacrificing himself to aid in your escape and kill Colonel Autumn, who injects himself with an anti-radiation drug before being hit with the radiation and thus survives.
You must then proceed through the Taft Tunnel to the Citadel with the remaining scientists. Upon leaving the tunnels and entering the safety of the Citadel you are introduced to Elder Lyons, leader of the Capital Wasteland's detachment of the Brotherhood of Steel, who grants you access to the Citadel. He also gives you permission to receive power Armor Training. You then find out that Vault 87 was another vault in the D.C. area that was issued a G.E.C.K.
Finding The Garden of Eden
Inside Vault 87 is Fawkes, a super-mutant that had access to the vault computers and their vast data banks, resulting in him being significantly more intelligent than the average super mutant or even human. He was trapped in the room by the other super mutants who viewed him as a freak, and prefers to be called a meta-human. Upon questioning him, he offers to take you to, and retrieve the G.E.C.K. from the irradiated section of the vault if you free him from his holding cell. If you choose not to free him, there is a room with a Radiation Suit and Rad Away which can be used to reach the G.E.C.K. After having Fawkes retrieve the G.E.C.K or doing it yourself, you start to head back to Little Lamplight, but are ambushed and captured by Enclave soldiers before exiting the vault with the G.E.C.K.
When you come to you find yourself in Raven Rock, an Enclave stronghold in the extreme northwest of the map, there Colonel Autumn questions you and asks you for the activation code to Project Purity. However, President John Henry Eden orders Autumn to come and talk to him. When the Colonel leaves, the President requests an audience with you and deactivates your restraining field. The President orders the Enclave soldiers not to harm you, an order which was promptly recalled by Colonel Autumn. You are then forced to fight your way through Raven Rock to Eden's office. You find that he is an advanced model of the ZAX Supercomputer and is actually an amalgam of all of America's former Presidents. He tells you that the only way to get humanity to function properly in the wasteland is through water. He also says that The Wasteland must be cleansed, which is why he does not allow you to leave until you have taken the vial of modified Forced Evolutionary Virus, which would kill all super mutants, Ghouls and wastelanders. You can then choose to destroy President Eden either through a speech check, Intelligence check, or find his self-destruct code and tell it to him. If you ask why Colonel Autumn cannot carry the F.E.V vial for him, Eden tells you that the Colonel does not agree with his plans. You may then leave Raven Rock. Afterwards, you find Fawkes outside, who came a little late to rescue you. You must then head back to Elder Lyons in the Citadel. If you decided you should infect the project with Modified FEV, the appearance of Fawkes is meant to make you see that it might not be such a good idea considering the fact that you have made such a loyal and powerful friend.
You meet Elder Lyons down in the Citadel's lab. When you arrive, a heated discussion between Scribe Rothchild, Elder Lyons, and Sarah Lyons is taking place. Rothchild argues that Liberty Prime is not ready for action, while Sarah is arguing that there isn't any time for another plan. Eventually, it ends with Lyons giving up and allowing Sarah, and Lyons' Pride, to go to the Jefferson Memorial with Liberty Prime. Once you arrive at Project Purity, you confront Colonel Autumn one last time, and decide his fate. Then, you are faced with many difficult choices; enter the irradiated chamber of Project Purity and sacrifice yourself, make Sarah Lyons go in your place, make Fawkes go in your place, or simply do nothing and let Project Purity explode around you. Along with this decision, you must also decide whether or not to put the modified F.E.V. vial into The Project Purity console or not.
About two weeks after the events of Project Purity, the Lone Wanderer awakes inside the Citadel. The Brotherhood of Steel has engaged in an all out conflict with the Enclave. The Brotherhood of Steel has won every single confrontation with the Enclave mainly due to Liberty Prime. The Enclave was expected to be in complete disarray but this does not appear to be correct as they seem to have limited communication abilities.
The Brotherhood of Steel prepares to assault an Enclave communication building at the Satellite Relay Station led by Paladin Tristan along with the Lone Wanderer and Liberty Prime. As the Brotherhood of Steel breaches inside the station, an orbital strike fires upon them resulting in the destruction of Liberty Prime. The Lone Wanderer breaks through the Enclave along with three Paladins to discover an encrypted piece of information. The Lone Wanderer returns the information to Scribe Rothchild at the Citadel.
The Player returns to the Citadel and Paladin Tristan informs the player of a new weapon, and you need to find the component, the Tesla Coil. He tells you it is located in Olney Powerworks. You also receive a Deathclaw Scrambler which turns Enclave controlled Deathclaws friendly.
The only way to the Power Works is through the Old Olney's Sewer system. After receiving the coil, head back to the Citadel and deliver it to Tristan.
Once you make your way through, you find the new weapon, the Tesla Cannon. Infiltrating the Crawler you finally reach a terminal. Here you make your choice:
Each will net its own reward.