I don't buy the Enclave deserter explanation for James. It's not impossible that there was/is another hightech facility somewhere on the East Coast (probably was because otherwise it would have made sense for James to go back). It could have been another Vault or even a Vault City (like the one from Vault 8).

As for the Enclave being evil, it's easy enough if you take into account what bad things Eden (on the radio) has to say about the Brotherhood of Steel. James knew that the Brotherhood tried to help Project Purity so he'd know Eden was lying about the Brotherhood (I liked that in Fallout 1 the Brotherhood wasn't popular and was considered as a threat, something that Fallout 3 played down and simplified quite a bit by making the Outcast faction). To anyone with half a brain (doesn't include Nathan in Megaton) it would be clear that the Enclave has an agenda and that the propaganda is meant to alienate the Brotherhood from the population of the Capital Wasteland. That is the opposite of what Three Dog is trying to achieve and it's obvious that Three Dog and James had a chat about the Enclave so James would know what to expect from them when they reached the Jefferson Memorial.

I can't see James as Enclave material. IMHO Project Purity is much too noble and selfless for a reformed Enclave scientist.

Horribly late to the party, sorry.

Skimming the thread, I don't believe I saw anyone suggest this: the Protagonist's mother - James' wife - was from Vault 101. I believe that she's the woman that armored Vault 101 Jumpsuit (in Moira's shop) was originally meant for; she never came back for it because she got involved with project purity, and then died giving birth to your character.

It would certainly explain why and how James might know the code to open the door to the Vault - and why the Overseer might agree to let James and his infant son enter the Vault and stay there.

And, the scouting reports on the Overseer's terminal in vault 101 actually mention two people staying in Megaton as "ambassadors" of sorts, at least for a while.

It's a fun theory, though I highly doubt Catherine was from Vault 101. There is no hint of this in-game, or in her back-story. Catherine was working on Poject Purity around the same time Moira was born. And has since perished.

James got into the Vault because they needed a doctor. You can even hear some flavour dialogue on the subject in the moment before you start the Escape! quest. As for the code, he was a very clever man, and where there's a will there's a way. James was also a scientist, he would have been more than capable of getting any information he desired.

The armoured Vault suit is more than likely tied to the scout party that was sent out in 2241, either belonging to Anne or Agnes. Most likely Agnes as she had closer ties to Megaton, being one of the two ambassadors.

Guys here is what happened. Dad did most likley grow up at Rivet city even though this is never confirmed. His BOS friend is star Paladin Cross. He got into the Vault because their doctor had recintley been killed on a mission outside the Vault and they were desperatly in need for a new one and now Jonas was born in the Vault.

Pretty doubtful. Even Doctor Li didn't come from Rivet City but first came there after Project Purity was over.

Moira doesn't seem old enough for that to be true.

If you talk to different Brotherhood members, you find out who it was, and it was not a guy, but a female. If your a good guy, she will even join you. This is all gathered from actual conversation with her.

I dont see Mom and Dad being Enclave deserters.

When the Enclave first arrives at the Jefferson Memorial, Dad says "It seems we have uninvited visitors, i dont know who they are or what they want".

When he speaks to Colonel Autumn he says something like "Colonel Autumn.....it is Colonel right ?" suggesting he does not recognize his rank badges because he isnt familiar with military ranks and just heard one of the soldiers calling him colonel.