The Wanderer is given a sample of the virus before leaving and returning to the Brotherhood of Steel, who had already learned that the Enclave was in possession of the G.E.C.K. Seeking to finish what the previous President wanted, it asks the Wanderer to instead use Project Purity to infect the area's water supply with a modified virus that would kill all mutants. The Wanderer eventually fights their way to the President, who it turns out was actually a sentient supercomputer. Learning of the strange development, Colonel Augustus Autumn instructs his troops to shoot the Wanderer on sight. In what was the start of a string of surprising twists, the Wanderer is freed from their cell by the Enclave leader, President John Henry Eden, who requests that they come to see him. Before they can escape, they are captured by the Enclave, who confiscate the G.E.C.K and take them to their base at Raven Rock. The vault had since come to be overrun by Super Mutants, but the Wanderer is eventually able to retrieve the G.E.C.K. The Brotherhood would later help the Lone Wanderer get to Vault 87, where a G.E.C.K. The Lone Wanderer then goes with Doctor Li and the other surviving scientist to the Citadel (the ruins of the Pentagon), where they seek shelter with the Brotherhood of Steel. James sacrifices himself to stop their leader, Colonel Augustus Autumn, from sabotaging the project, but not before asking the Wanderer to escape and finish his work by finding the G.E.C.K. They then go to the Jefferson Memorial with a group of scientists, hoping to continue their work on Project Purity, but the place is invaded by Enclave soldiers. The Wanderer frees James and together they return to Rivet City and James reveals that he had been after a device known as the Garden of Eden Creation Kit (G.E.C.K.), which he needs to complete Project Purity. Next, the Wanderer explores the Jefferson Memorial before finally tracking James down to Vault 112, where he was being held captive by its Overseer, Dr. Conceived by the Wanderer's parents, the project had experienced a big setback after Catherine had died and James had decided to go raise their newborn child in the safety of Vault 101.
Doctor Li tells the Wanderer about Project Purity, a plan to purify all the irradiated water in the nearby Tidal Basin and Potomac River.
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