James was born in 2226. Later in his life he formed or met a group of scientists. One of these scientists was Dr. Madison Li, one of the most intelligent humans in the Capital Wasteland. Another was Catherine, who quickly became the love of his life. Catherine had a dream, a dream of purifying water and then giving it away, to any and all. This became the groups main project and was soon dubbed Project Purity. James was the chief scientist and project leader of the ambitious project. It intended to cleanse all of the radioactivity from the water of the Potomac River that fed into the entire Capital Wasteland. However, when his wife died after giving birth to the Lone Wanderer, he gave up on the project over the grief of losing her. He then asked for entry for himself and his child into Vault 101 in return for becoming the Vault's new physician, and the overseer granted his request.
James became the Vault's new physician, a job he could easily handle. He didn't really like the vault, but stayed to raise his child in a safe environment. James never forgot about Project Purity or his deceased wife. He even had the biblical revelation that inspired the project framed, he hung it on the wall in his office and placed one in his apartment. He tried to do the best he could for his child, holding birthday parties for the Lone Wanderer, giving the Wanderer a BB gun and setting up a place that the Lone Wanderer could use the BB gun. Something which the Overseer wouldn't agree with if he found out about it.
Return to the world above
In 2277, James planned to return to the surface, leaving his child in the Vault to be safe and happy. His assistant Jonas had planned to have gone with him but was tortured and then killed by Officer Mack. Even though James had planned to leave his child in the Vault, the Lone Wanderer escaped and followed the trail of his father. James first went to the small town of Megaton to visit Colin Moriarty. James met Colin several years ago on his way to the Vault. He asked Colin what's been happening in the wasteland since he entered the vault and Colin tells him about Galaxy News Radio. James left in a hurry and managed to make his way through the ruins of Washington, D.C. and reaches the GNR Building Plaza, where he then talked to Three Dog. Three Dog told James what had been happening recently in the wasteland and then James left to find Dr. Li. Arriving at Rivet City, he asked for Madison's help to restore the project but she declined. Then James heads of to the old lab at the Jefferson Memorial. James soon found out he needed a Garden of Eden Creation Kit. He marked his way to Vault 112 to find Stanislaus Braun, the creator of the G.E.C.K and to gain knowledge about it. James arrived at Vault 112 and entered the Tranquility Lane simulation. He talked with Braun but doesn't want to play any of Braun's games so Braun traps him in the body of a dog named Doc. The Lone Wanderer arrived in Tranquility Lane and soon rescued their Father. After a talk the two return to Rivet City. At Rivet City, James successfully recruits Madison Li and her team and they head to the Jefferson Memorial. After arriving at the memorial, the scientists soon get things back on track, but then the Enclave arrive.
The Ultimate Sacrifice
Augustus Autumn entered the facility under guard of Enclave soldiers. He locked the activation room and begins to threaten James, demanding he hand over the activated Project Purity. James explains that the project isn't yet functional, much to Autumns dismay. After being brow beaten, James submitted, causing a disruption within the activation room. This caused a massive radiation leak that kills everyone inside other than Autumn. James then falls to his knees, his final word: "Run" aimed toward his child. James then collapsed and died in the project control room.
Baby Steps: James puts the one-year old Lone Wanderer in a playpen in their room which contains the You're S.P.E.C.I.A.L.! book. After a brief absence, James returns and shows the child Catherine's favorite Bible quotation, and takes his child to Amata.
Growing Up Fast: James has a small conversation with the Lone Wanderer at the beginning of their tenth birthday party, and later in the party gives them a BB gun as a birthday gift, and tasks them with killing a radroach.
The Waters of Life: Father and child make their way first to Rivet City, then to the Jefferson Memorial, the site of Project Purity. As the Enclave storms the Memorial, James refuses to cooperate with Colonel Augustus Autumn. In the end, James floods the room with radiation, attempting to kill Autumn but killing himself in the process, with no success in his objective. The last time the Lone Wanderer sees him is when James presses himself against the glass door of the activation room, and telling his child to "Run!" as he falls to the floor, sacrificing himself so his child could live.
Effects of player actions
When the player is doing tasks to make Project Purity work, James will say that he heard of the player's actions. His reaction will change depending on how you resolved the quest The Power of the Atom. If you disarmed the bomb, he will ask you if you truly did it, and will be proud of you if you say that you did. If you caused Megaton's destruction and admit it to James he will be disappointed (you can lie to him, but he won't really believe you unless you have very high Karma).
If you did not resolve the Power of the Atom quest at all, or if you talk to him again after he comments on the aforementioned quest, he will instead comment on your current Karma level. If you have good Karma, he will say "You're a good person, and it shows". If you have bad Karma, he will instead comment on how you "seem troubled, like there is a cloud hanging over you." If you have neutral Karma he will simply greet you in the default manner.
Birth scene: James delights over the birth of his child, presenting the child to his wife, who expresses pride and happiness before going into cardiac arrest. James then attempts, unsuccessfully, to save her life.
James counts as a "companion", and as such will use up ammunition on any non-companion weapon (unlike most non-player characters, who have infinite ammunition).
Neither James' nor Catherine's surnames are known or stated in gameplay, thus allowing the player the freedom to choose his or her own surname.
It seems that James has a preference for Scotch. According to Project Purity Personal Journal #5, he mentions having downed "half a bottle of Scotch" the night he broke into the Overseer's computer. When visiting his living quarters at Project Purity, the player can find a number of empty Scotch bottles around James' living area.
In Vault 101 he has brown hair, in the Wasteland, his hair is gray due to aging.
The unused skin of Doc seems to be a German Shepherd, considering Stanislaus Braun is German. Also, it seems that the dog has different eye color - similar to Dogmeat.
James may not follow to the Jefferson memorial if you fast travel.
The player can show contempt for James, by saying to him, "Fuck you, Dad." Also, when Star Paladin Cross asks about him, the player can say that he "lived as he died," as an "asshole." Yet James simply says he's "sorry you [the player] feel that way" about the former.
When you go to Vault 106 after James dies the player will have illusions of him walking around the vault as if he were still alive.
"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."
"As far as I can tell, you're a perfectly healthy 16 year old boy/girl, so yes you have to go to class to take your G.O.A.T. exam."
"Son/Honey, I brought you into this world, I think you know the rest..."
James is voiced by actor Liam Neeson, after whom the character is also physically modeled. "This role was written with Liam in mind, and provides the dramatic tone for the entire game. "Liam is absolutely amazing to work with," said Todd Howard, Executive Producer of Fallout 3. "It’s been a pleasure bringing the father to life and working with the wonderfully talented people at Bethesda on Fallout 3," said Neeson. "I hope the fans of the franchise and the game will be excited by the results."
ps3 - On the way back to Rivet City from Vault 112, he will sometimes get stuck while traveling with him. If this occurs, fast travel to Rivet City and wait 24 hours in the Science Lab. He will appear and start talking to Doctor Li.