Project Purity

 ''I am Alpha and Omega, the beginning and the end. I will give unto him that is athirst of the fountain of the water of life freely.'' -Revelation 21:6

is a water purification project that began before the beginning of Fallout 3. It was originally supported by the Brotherhood of Steel, although they soon abandoned the project due to dwindling manpower. In Rivet City, Doctor Li will tell the Vault 101 Dweller that his father, James, left Vault 101 to travel to Rivet City to start the project up again. Dr. Li refused and James moved on. Project Purity is what motivates your father to eventually leave the Vault in search of a GECK in the hope of completing the project.

After finding James, it is revealed Project Purity was rekindled at the Jefferson Memorial, but the location was captured by Super Mutants. After enlisting the assistance of Doctor Li and her staff from Rivet City, the location is cleared before the project finally resumes progress. However, the Enclave seizes the Jefferson Memorial and attempts to persuade James to cede control to the Enclave. James refuses, and kills both himself and the Enclave soldiers with lethal doses of radiation. The player is forced to escort the remaining staff to the relative safety of the Citadel, contending with Feral Ghouls and even more Enclave soldiers.

Though the Enclave managed to capture the memorial, a crucial component, the GECK, is still required to bring the project to fruition. Once the Vault 101 Dweller does obtain the GECK, they are incapacitated by the Enclave and taken to Raven Rock. President John Henry Eden demands that the Vault 101 Dweller install the modified FEV virus when they reach the Project Purity control room, which will purge the Capital Wasteland of any beings "tainted" with radiation, regardless of severity. The Vault 101 Dweller battles his or her way to the control room, where a final decision is posed. The Vault 101 Dweller will either choose to insert the modified FEV virus, fulfill the original intent of Project Purity, or allow Sentinel Lyons to execute the latter. As a result of James's actions, the Vault 101 Dweller ultimately dies if they choose to enter the control room.

After the decision is made, the water of the Wastelands is purified at last, and life begins anew in the Capital Wasteland. The Vault 101 Dweller can also, if he/she chooses, simply not do anything and sacrifice the lives of everyone in the facility for no reason. The ending that follows is shorter than the normal ending.

Quotes

 * The plan was to build a facility that could purify all the water in the Tidal Basin at once. No radiation, no muck, just clean fresh water. - Doctor Li

Related quests
The project is tied to Following in His Footsteps, and possibly tied to The Waters of Life, as well as the Jefferson Memorial location.