After James is found, Project Purity can be put back on track, but the reunion is cut short when the Enclave commander, Augustus Autumn, arrives demanding control of the project. James, unwilling to allow the project to fall into the hands of the Enclave, sacrifices himself by filling the control chamber with deadly amounts of radiation, hoping to kill Colonel Autumn and the other soldiers in the process. The colonel manages to survive, however.
After fleeing from the Jefferson Memorial, the Wanderer takes refuge within the Citadel and enlists the help of the Brotherhood of Steel to retrieve a G.E.C.K. from Vault 87 for the restoration of Project Purity. After retrieving this G.E.C.K., the Wanderer is captured by Colonel Autumn and taken to Raven Rock. There, John Henry Eden presents the Wanderer with a canister of modified FEV for insertion into Project Purity, which would poison any mutated creature drinking the purified water. The Wanderer refuses and escapes, sabotaging Raven Rock in the process. After finally stopping Colonel Autumn, the Wanderer and Sentinel Lyons are faced with the dilemma of who would re-enter the radiation-flooded Memorial and activate the purifier. Once this decision is made, the Wasteland is finally given the greatest gift of all: a constant source of clean water.
Broken Steel The Lone Wanderer awakens two weeks later to face the consequences of their decisions so far and joins the Brotherhood as a knight, in their mission to distribute the newly-purified water and to hunt the Enclave remnants. This hunt would eventually put the Wanderer in control of an orbital strike. The Lone Wanderer either uses it to destroy the Enclavemobile base crawler or the Citadel. During or after the events of Fallout 3, the Lone Wanderer travels to various places such as The Pitt, Point Lookout, Mothership Zeta and participates in a simulation of the Anchorage Reclamation.
By 2297, the Lone Wanderer had disappeared from the Capital Wasteland, and their fate was unknown. Most citizens of the wasteland had a story about the Wanderer, and many of his or her actions had gone down as local legend. History had even forgotten whether they were a man or a woman. Much of the documentation of their actions had however became flawed, and were riddled with conflicting reports. On the 10th of September, Moira Brown began work on a biography of the Lone Wanderer.