The Waters of Life

The Waters of Life is the eighth main quest in Fallout 3. It is also an Xbox 360/PC achievement and a PlayStation 3 Trophy.

Go to the Rivet City science lab and join the scientists at Project Purity
James will make his way to Rivet City; the Lone Wanderer can choose to follow him there or leave him on his own, either way, he will eventually reach the Rivet City science lab and wait for the player character to meet him there.

Upon the player character's arrival, James convinces Dr. Li to reactivate Project Purity. After a short conversation, he asks the player character to meet him and the scientists at the Jefferson Memorial. It is highly advised to stock up and prepare for a battle, as well as free up as much inventory space as possible.

Characters
Named characters who relocate to the Jefferson Memorial:

Clear Project Purity of any remaining mutant threat
Dr. Li, James, and the rest of the science team will be waiting for the player character at the entrance to the Gift Shop. James informs the player character that they must clear the Memorial of the remaining super mutant threat before they can proceed. The Memorial Sub-basement consists of short narrow corridors with an occasional room.

If the player character has already cleared out the Jefferson Memorial, James and the team will go straight to the Rotunda, bypassing the preliminary pep-talk.

Routine Maintenance
Once James arrives at the control room, he asks the player character to carry out some maintenance tasks to bring the project back online.
 * Turn off Flood Control Pump Power - The Flood Control Pump is located in the sub-basement level in a room to the left of the bunk bed area. The switch is beside an intercom and is illuminated by a floodlight.
 * Get the fuses from Dad / Replace Damaged Fuses - Return to James to get new fuses. The fuse box is at the end of the basement area: there are signs on the wall ('Fuse Access A1') to direct the player character to the fuse box.
 * Boot up the mainframe / Speak with Dad over intercom - The door to the mainframe is located on the 'upper level' of the basement, before the stairs down to the bunk bedroom. After the fuses are installed, a large green light beside the door will turn on. The player character must enter the door and throw the switch on the mainframe, and then speak to James. He will tell the player to return, then change his mind and tell the player character to clear out a blockage in an intake pipe.

Drain the Intake Pipes
The entrance to the pipes is directly ahead from the entrance to the Gift Shop. Once inside, the player character must run through the pipe to the end and turn the control. On the right is the valve to activate the draining. At this point, as soon as the valve is activated, the player character will witness the arrival of Enclave soldiers in a Vertibird. (If from inside the pipes one successfully attacks one or more of the arriving Enclave soldiers then upon the next section of pipe they may be waiting at the end of the tunnel.) The opposite gate unlocks, and the player character is allowed through to the next area.
 * Note that if one tells any companions to "Wait" in the control room, they will immediately die upon activating the valve.

Return to the Control Room
Now the player character must battle their way back to the Rotunda, killing any power-armored Enclave soldiers in the way.

Upon arriving at the control room, Dr. Li is locked out of the main area, while Janice Kaplinski, James, Colonel Autumn and two Enclave soldiers are locked in. Colonel Autumn confronts James and orders him to forfeit the Memorial and assist the Enclave with making the water purifier operational. James refuses, stating that the Enclave has no authority over such a private project, and asks the Colonel to leave. Autumn eventually kills Janice Kaplinski, prompting James to accede to the Colonel's demands to avoid more violence.

James instead overloads the purifier, flooding the locked chamber with deadly levels of radiation. Col. Autumn quickly injects himself with a mysterious solution and keels over, unconscious. James drags himself over to the emergency bulkhead and tells the player character to run, before slumping to the ground, dead.

Escort Doctor Li to the Citadel
A stunned Dr. Li informs the player character that the only way to escape the Memorial is through a series of underground tunnels that lead to the Brotherhood of Steel stronghold, the Citadel. She will run to a manhole in the floor not far from the rotunda door, and the player character must follow. Once in the Taft Tunnel, she will tell the player character that they must keep moving to avoid detection by the Enclave. Daniel Agincourt can be given a pistol to aid against the Enclave. Doctor Li will follow or wait depending on the player character's orders; however, it is important to note that she will also move forward automatically if one gets too far ahead, stopping at designated points in order to keep up.

The tunnels are populated with Enclave troops and multiple variants of feral ghouls. The first area with catwalks houses a table with various Chinese items: including a Chinese Army: Special Ops Training Manual, a Chinese Assault Rifle, a dirty Chinese jumpsuit, and a rare Chinese commando hat. Also past the table is another table with a rolling pin like the one found in Tranquility Lane.

Once in the second section of the tunnels (called Taft Tunnel), Garza can be heard saying, "Dr. Li, my heart... I must rest." then Dr. Li will explain that they need to stop: Garza's heart disease has gone critical, and he will not make it to the Citadel alive if first aid is not administered quickly. The player character has a few options at this point:
 * Give up five stimpaks to alleviate his condition until he can see professional medical care (this awards good Karma).
 * Convince Dr. Li to leave Garza behind.
 * Convince Dr. Li to give Garza three bottles of Buffout instead, to drug him and keep him moving.
 * Convince Garza it is best to stay behind.
 * Kill Garza (results in negative Karma).
 * Note that killing Garza with a gun will result in Dr. Li refusing to move forward, making the quest impossible to complete.

If the player character does not want to leave or kill Garza but does not have the stimpaks nor Buffout, they need to find stimpaks elsewhere and bring them back to Garza. They are in two locations: the first is an abandoned operating theater which is to the left when the corridor forks off not long after Garza has to stop; the second location is at the very end of the corridors, directly behind the Brotherhood of Steel barricade, in a first-aid container.

Alternatively, the player character can simply fight their way through the tunnel, leave it, and go find the supplies somewhere else (buying them from a doctor would be the simplest way). Then, head back to the Citadel, enter the tunnel, and head back to the area where the scientists are. They should still be there, and one should still be able to give Doctor Li the medical supplies and complete the quest as normal.

If Garza is already dead before The Waters of Life is started, this part of the quest will be skipped entirely.

After dealing with the Garza situation, the player character can continue the same routine of checking for danger, telling the scientists to wait, then returning to the them once their path is secure. Eventually, the player character must enter a room with a catwalk above the entrance. This can be a tricky battle since the Enclave troops have high ground, complicated by the fact that non-player characters have a tendency to run inside the room and stand in the center (especially followers like Charon).

Although soldiers on the upper levels are not normally accessible, it is possible to reach their location by using the steps, jumping onto the railing, then running along the wall to reach them. This also allows for looting their power armor (Enclave Hellfire armor with Broken Steel active or Tesla armor). In the housed area to the back of the room is a desk with an eyebot helmet.

Farther down the passage, the opposition will turn into feral ghouls. Eventually, the terrain will become a sewer tunnel with a Brotherhood of Steel checkpoint at the end. The soldier is not too happy to see civilians running through his checkpoint. Once past the sandbags, it is advised to keep running until the rest of the science team is well away from the sandbags, as a horde of feral ghouls will pour from a near door. The Brotherhood of Steel is armed with a flamer for this exact reason and will pour flame into his attackers while two overhead turrets help out. At the start of this tunnel on a bench is a Nuka-Cola Quantum and a copy of Nikola Tesla and You on a picnic table behind a generator. If the Brotherhood of Steel trooper is killed, one of the scientists will likely then pick up the flamer and attack the feral ghouls.

Once topside, an exasperated Dr. Li will argue with Paladin Bael for entrance into the Citadel to no avail. She then runs to the intercom and yells at Owyn Lyons to open the "goddamn" door at once. The door then immediately opens.

Once inside, Owyn Lyons will confront Dr. Li and the surviving science team. Lyons questions Li for a few minutes on what transpired at the Memorial, and Li breathlessly tells him about James's plan and the Enclave's intervention.

Bugs

 * After James poisons the control room, Autumn will occasionally not inject himself and die, not moving for as long as one watches him.
 * The path the group takes from Rivet City to the Jefferson Memorial leads them past an outpost where a group of super mutants may spawn. Though normally they will be out of their way, the super mutants may catch sight of them and attack, in which case the scientists and escort except for Dr. Li and James may be killed.
 * The scientists may not spawn properly as the player character follows them out of Rivet City. This can be fixed by re-entering the previous location and then going back, but may cause the group to be broken up as they travel. Alternatively one can fast travel to Jefferson Memorial and should link up with them again.
 * Right after Dr. Li confronts the player character about Garza's condition, regardless of the response given to her, if the player character chooses to go back where Garza is, it is possible to see companions spawned there when they should be waiting for the player character in the Megaton house.
 * If there is a dead super mutant in the Jefferson Memorial doorway, the entire team will enter the building except for James, who stands in front of the Project Purity entrance in the wasteland and tells the player character they need to go to Project Purity. This bug stops the quest and game from being able to be completed. Beating him there and moving the body out of the way appears to resolve the issue. Or you could knock James unconscious and drag his body to the door of the rotunda and most likely he will enter and the quest will continue.
 * On the way to the memorial, Dad may tell the player character to check for super mutants. Once the area is cleared, he may be stuck in the air unable to be talk. The quest can still be completed and this Dad may still be alive during the Take It Back! quest.
 * If the player character hacks the terminal before Dr. Li, or simply does not allow Dr. Li to hack the terminal, one may get a bug just outside the "catwalk room" where the player character fights off the Enclave while Dr. Li opens the door. After the threat is cleared and the door opened, Alex and Daniel continue to wait endlessly on either side of the doorway. Dr. Li and Garza still follow the player character normally. Alex and Daniel remain in the same place even if the player character goes to a different area and returns. Alex and Daniel will return to the Jefferson Memorial after the main quest if Broken Steel is installed.
 * If the player character tells Doctor Li to lead the way, she may get stuck at a certain point and not move. This can be fixed by killing Doctor Li and entering the sub-basement while she is dead. Wait 1 game hour then go back to the gift shop and Doctor Li will have entered the secret tunnel. Alternatively, the Citadel glitch can be used to prematurely enter the Citadel, and then reading the Vault-Tec terminal's entry on Vault 87 triggering Picking Up the Trail, bypassing the Waters of Life quest altogether.
 * When James and Doctor Li talk in the Rivet City science lab, the cinematic mode will not come on and the player character is free to walk around like normal, yet their conversation still goes on.
 * When one clears out the areas in "Project Purity", it may happen when everyone enters the Jefferson Memorial they will not move but stay at the door and talk with one another. To fix this one must repeatedly walk into James until they get near the rotunda door then he should walk in by himself.
 * If one reaches the rotunda quickly they may be able to get behind the doors before they shut; one will die of radiation poisoning if this happens. However, if the player character attempts to talk to Colonel Autumn, there will be no dialogue from him and he will shoot Janice after exiting the non-existing dialogue. This will cause the cinematic to halt completely, and one will be able to talk to James and the two Enclave soldiers accompanying Autumn, as they will not turn hostile even after shooting Autumn, who will not die regardless. The player character will, however, be stuck in the control room as the bulkhead will not open.
 * The four quest companions one guides through Taft Tunnel seem to mess up the game's standard companion handling. Examples: one or more of standard companions spawn in the tunnel; one of the four quest followers turns into Dogmeat; Dogmeat will relocate to Vault 101 after one reaches the Citadel. Any spawned followers may remain in their waiting state in the tunnel, so if one is missing any after this quest, look for them in the second part of the tunnel.
 * Sometimes, Dr. Li will stay near the entrance to the Taft Tunnel and refuse to progress to the Citadel. This can be remedied by using the console to disable then enable Doctor Li. (Disabling/enabling may not help if all companions but Garza are alive, disallowing the game to progress at all.)
 * After turning off the pump and run back upstairs to get the fuses, Dad always comments on what the player character has done up to this point. If The Lone Wanderer blew up Megaton and choose the option "what I do in the world is my business, not yours," he will respond with: "What you do in the world may be your business, but here, with me, you are MY son." He says "son" even if you are his daughter.
 * Sometimes if one rushes through the game and get to where they have to get the fuses from James, he will just keep repeating Revelation 21:6 and will not let the player character progress through the main storyline.
 * Sometimes if the player character accidentally harms a follower other than Doctor Li, when arriving at the Citadel the non-player character will become hostile towards the player character causing the Brotherhood of Steel to also become hostile. This can sometimes be fixed by reloading an autosave, activating a Stealth Boy then killing the non-player character.
 * After Dr. Li demands the door to the Citadel be opened the player character will have a chance to enter the Citadel before they are supposed to. This sometimes leads to Dr. Li not being "escorted" into the Citadel, and permanent cut-scene immobility should the player character re-enter at a later date to try and complete the main quest. This can sometimes be fixed by heading to Little Lamplight and the next plot sequence.
 * If the player character uses the Mesmetron on any of the scientists in the rotunda the NPCs start glitching out in various ways. Doctor Li will start running in mid-air outside the control room in the rotunda, hit the wall then warp back and repeat. Also, James may become hostile and start shooting at the player character and/or Doctor Li.