James seduced the Overseers wife, and she let him in the Vault, and Amata is your half-sister, and that's why the Overseer hates both of you. End of story.
that would be messed up in many many ways.
synopsis of Vault 101 (purely theoretical)
1 Star Paladin cross Is your mother, when using Toggle free cam and looking at your birth mother she is of african american decent. she never died
your father told you she died because she left the vault and he's supposed to keep up the facade of an impenetrable vault life. you would ask well why do moiriarty and Dr.Li say she's dead
maybe it is presumed she's dead by Dr.Li, she does state your dad simply up and left after you were born, maybe her death was faked, where after wards she accompies him and yourself to megaton in Power Armor to support herself during the long journey ( remember she just gave birth, how she got the armor? remember that the BOS protected jefferson) once they reach megaton James wife no longer accompanies them still wanting to make a difference out in the wastes while her husband, your father cares for you in the Vault (maybe she did not trust the whole idea of the vaults*) where she then joins the BOS.
Vault life: we already know the whole set about this, dad gives some sob story about his dead wife and only son, gets into the vault only if he serves as a Doctor, at that time Vault 101 suffers a major incident that changed the Personnel (new overseer, the overseer we see now was not the original 19 years ago) and created a zealous fear about opening the vaul. most advlts and maybe children go missing and or killed, the newborns are told lies and the advlts are brainwashed. (brainwashed being how scared they are of the opening doors, remeber the guards)
After the vault: your mother now star paladin Cross: notice how she is so eager (on good karma) to join with you and protect you and makes comments now and again about your father & how proud he would be. she acts motherly and is the right age between the length of time since you were born.
Inconsitencies(sp)---- If this were true why didn't she join with your father once he left the vault and started project purity?
A. well your father didn't go to the BOS citadel much less knew where your mother was at that time, since he went around asking for updates on the land from threedog and moriarty. & by the time you do arrive at the citadel your father is already dead and gone
-- Alright if pops is dead why didn't mom just fess up about who she was?
well one reason could be dependant on your karma level, remmeber the Wasteland changes people so
in the instance that you were the [censored] of the land why would mom tell you who she was?
---OK I am not a [censored] I am an angel why wouldnt she tell me who she is if she was really my mom?
like i said before the wasteland changes people maybe she felt she was no longer the woman that gave birth to you those nineteen years ago maybe she felt it was easier not telling you the truth so that she could protect you better and not jeopordize your function out in the wastes.