This spans from classic Who to the tv movie and up to Tennantâs run if not later. It explains a few things.
The Doctor was a Gallifreyan, an alien to us on Earth. That is, he was untilâ¦
Ace goes on after her adventures with Doctor 7 to become the first non-Gallifreyan Time Lord. She later meets a man known to us as The Other and the two of them become a couple. They marry and live on Gallifrey, but to avoid persecution from the increasingly agitated (Gallifreyan) Time Lords, they travel back into the planetâs relative past, settle down, and have a child.
This child is half human, on his motherâs side. They name him after their illegal paradox of a trip as a reminder of how fragile time and space really are, but cannot give his name to anyone. As he grows older, he takes on the name Sigma Theta, and eventually, through encouragement, takes on his own moniker as âThe Doctorâ. Thus Ace fulfills the âgreatnessâ Seven saw in her, and the Eighth Doctor doesnât lie in the TV Movie.
Then the Time War happens. Time is rewritten over and over, Ace and The Other are lost to time, and The Doctorâs origins are rewritten with it all, rendering him a full Gallifreyan again. You see, he NEEDS to exist because he has been a crucial part of several âfixed pointsâ in time/space, thus no matter his origins, the universe, the Time Lords, or perhaps even the time stream with help from the Tardis makes sure he exists, no matter what his origin is.
The next time we see Ace, it is in the episode End of Time, where she has been caught by Rassilon. She and another unnamed Time Lord/Lady are punished for their crimes by way of transformation into (possibly the first) Weeping Angels. The two are sent to the beginning of time to become the Weeping Angels of old, where there is no way for the Angels to âfeedâ (they feed by sending people back in time, remember) and thus their suffering begins. As stone, they can never die (like Time Lords).
So yes, the Woman is the Doctorâs mother. But is also Ace. And sheâs human. And sheâs a Time Lord. And itâs all wibbly wobbly timey wimey.