The Waters of Life

The Waters of Life is a main quest in Fallout 3 as well as an achievement/trophy.

Synopsis
Now that James is free from Vault 112, he, Madison Li, and her team can revive Project Purity. The Lone Wanderer is asked to assist in reviving the project, starting with clearing out the super mutants.

Walkthrough
"Autumn: By the authority of the President, this facility is now under United States government control. The person in charge is to step forward immediately, and turn over all materials related to this project.
 * The quest first requires the player to meet up with James at the Rivet City science lab, located in the aft section of the ship. Madison Li will be surprised to see James nearly 20 years later, still aching to complete the project he once abandoned, but after a short persuasion, she will agree to join his party. The player is asked to come as well, to the Jefferson Memorial. The team will set out from the science lab and walk over to the Memorial, with James and Madison Li at the head and Anna Holt, Janice Kaplinski, Daniel Agincourt, Alex Dargon, and Garza also coming along.
 * The characters are all marked as essential, which is a good thing, since there are likely to be super mutants near the memorial. Most of them will flee if attacked, leaving it up to the player to mop up. To reach the next stage, the player needs to go through the Memorial and kill any super mutants inside. Given the confined quarters, melee weapons, automatic guns, and shotguns work well. If the player cleared out the Memorial beforehand (during eg. Scientific Pursuits), then James and his team will enter.
 * The next step is maintenance. James will take position in the control room and ask the player to perform maintenance. James will give directions to each location, but players should keep in mind they're always relative to the entrance door to the sub-basement, not the location where the player has to apply the fix. Fixes include:
 * Turning off the flood control pump power, located to the left of the living quarters (bunk beds). The switch is by the intercom, lit up by a floodlight, and James will talk to the player once this task is accompanied.
 * The next step is replacing fuses. The player has to come back to James for spare ones, then find the fuse box in the basement. The location can be easily found by following the signs (Fuse Access A1).
 * Finally, the player has to boot up the mainframe, located on the top level of the basement, inaccessible before installing the fuses. Simply entering the mainframe chamber and throwing the switch will complete this objective.
 * At this stage, James will ask the player to clear the blocked intake pipe. Note that talking to James will lock all exits from the memorial and disable the Memorial fast travel marker, locking the player in. The entrance to the intake pipe is located just ahead of the entryway to the Gift Shop. Simply crossing the length of the pipe and activating the valve will complete this objective.  The Enclave arrives just as the player turns the valve and the Memorial becomes inaccessible for the remainder of the main story, so anything left behind will be lost permanently. At any rate, the player cannot go back, so they need to head through the gate and then fight their way back to the control room in the Rotunda.
 * At the rotunda, the control room will be locked, with James and Janice Kaplinski apprehended by Colonel Augustus Autumn and his bodyguards in full Enclave power armor. The Colonel demands full compliance and handing over the purifier to the Enclave. James refuses to budge.

James: That's quite impossible. This is a private project; the Enclave has no authority here. I'm going to have to ask you to leave at once.

Autumn: Am I to assume, sir, that you are in charge?

James: Yes, I'm responsible for this project.

Autumn: Then I repeat, sir, that you are hereby instructed to immediately hand over all materials related to the purifier.

James: I'm sorry, but that's....

Autumn: Furthermore, you are to assist Enclave scientists in assuming control of the administration and operation of this facility at once.

James: Colonel... Is it Colonel? I'm sorry, but the facility is not operational. It never has been. I'm afraid you're wasting your time here.

Autumn: Sir, this is the last time I am going to repeat myself. Stand down at once, and turn over control of this facility.

James: Colonel, I assure you that this facility will not function. We have never been able to successfully replicate test results...


 * The Colonel interrupts James by shooting Janice Kaplinski.

Autumn: I suggest you comply immediately, sir, in order to prevent any more incidents. Are we clear?

James: Yes, Colonel. I'll do whatever you want; there's no need for more violence.

Autumn: Then you will immediately hand over all materials related to this project, and aid us in making it operational at once.

James: Very well. Give me a few moments to bring the system online."


 * Instead of activating the system, James decides to commit suicide, taking Autumn with him. As he dies of massive radiation exposure, however, Autumn injects himself with a mysterious plot device, before falling down unconscious. If their ragdolls fall close to the bulkhead, the player can manipulate the camera in third person to loot both, gaining Autumn's unique coat and Dad's wasteland gear. This does not change Autumn's appearance later in the game.

Flight to the Citadel

 * Stunned by James' death, Li will tell the player that the only escape route leads through the underground tunnel and automatically move to the manhole leading down to the Taft Tunnel. The player has to follow and evacuate the surviving science team through the tunnels. Although Li stresses that the team has to keep moving, she can be told to wait. If the player moves too far ahead, she will move to pre-set waypoints and catch up along the next waypoint.
 * The player can hand Daniel Agincourt a gun, but keeping him unarmed is better if one intends to keep him alive for the duration of the evacuation. The rest of the team
 * The tunnels are essentially a gauntlet of Enclave soldiers, feral ghouls, and other attractions. The best way to negotiate the tunnels is to simply move slowly and patiently clear out each room. Some troops are located on inaccessible ledges and catwalks and can be impossible to loot without gibbing their limbs with explosives or knocking them down. The player can stock up on a large number of Enclave power armor and its Tesla variant, laser rifles, plasma rifles, and even find an old Chinese listening post with a Special Ops training manual, Chinese assault rifle, a dirty Chinese jumpsuit and the Chinese commando hat.
 * In the second part of the tunnels, Garza will start suffering from his heart condition. The player has several options at this point:
 * Give him five stimpaks to suppress his condition long enough until they reach the Citadel (good karma).
 * Persuade Li to cut him loose.
 * Persuade her to drug him with three doses of Buffout.
 * Persuade Garza to stay behind.
 * Kill Garza (evil karma).
 * It's possible to leave the entire team behind while they're busy with Garza, leave out the sewer by the Citadel, then collect the required items across the wasteland. They will patiently wait for the player. There's also an abandoned infirmary near where the team stops, and another first aid box behind the Brotherhood barricade.
 * Either way, the second part of the Taft tunnels is split between Enclave soldiers and feral ghouls. The Enclave soldiers are at their most difficult in the chamber with an overhead catwalk, as they set up a killing zone using their high ground advantage. Patiently taking them out and looking out for scientists that might come charging in is recommended. The second part is filled with feral ghouls that spawn once the player reaches the Brotherhood checkpoint. They spawn behind a nearby door and attack the strongpoint, with the flamer-armed soldier and two turrets engaging them in battle.
 * Note that there's a Nuka-Cola Quantum and a copy of Nikola Tesla and You on the bench near the start of the tunnel.
 * The quest ends at the gates of the Citadel, where Dr Li won't have Paladin Bael's lip and demands that Elder Lyons let her and the others into the Citadel. Lyons complies and meets Li at the entrance in the Bailey, receiving news of Project Purity's seizure, James' death, and the return of the Enclave. With access to the Citadel the quest ends, giving the player the opportunity to learn how to handle power armor, turn in holotags, and advance the story.

Bugs

 * It's possible for companions to spawn together with the science team at the "Garza" stage. This is one of many general bugs related to follower handling, which includes relocating companions to their starting position, spawning them in the tunnel only for them to remain there indefinitely, and so on and so forth.
 * It's possible for Alex and Daniel's script to break if the player hacks the terminal before Dr Li or prevents her from doing so outside the Enclave catwalk ambush, where she's supposed to open the door.
 * It's possible to aggro one of the science team followers, which will in turn cause the Brotherhood to become hostile. Reloading is the best fix, otherwise the player may have to resort to Stealth Boys and stealth kills.
 * Fast traveling away from the Citadel before the quest concludes and the team enters the Citadel can break scripts, making it impossible to continue, or even crash the game. Reloading an autosave or just completing the quest as normal helps. It's also possible for Li's scripting to break, necessitating a reload or disabling/enabling her via console.
 * The characters are prone to spawning and pathfinding bugs. Reloading saves, fast traveling to the Memorial, and so on helps ensure they all arrive where they should be.
 * It's possible for Janice to spawn outside the control room, breaking Autumn's script as the AI is supposed to shoot her. Exiting and re-entering the Rotunda at the start of dialog or simply reloading before entering can help.