The Master may be returning to Doctor Who in the most shocking way possible
So the first thing that this could mean is that Ms. Flood has been replaced. In the correct timeline, Lucy Saxon (I'm just going to assume Lucy is in charge for the sake of simplification) has either disposed of and replaced Ms. Flood, or mind-controlled her. Ms. Flood then spends her time watching out for the Doctor and making sure events go as they're supposed to.
This would explain why, in the wrong timeline, Ms. Flood seemed to only notice the TARDIS as it was leaving and she seemed absolutely terrified by it, dropping her groceries. Also, all the things outside her home for sitting and watching are gone. In this timeline where the plan failed, they may have never needed to swap her out.
Though, secondly, this could also lead to the possibility that Ms. Flood, herself, is the Master or some other character that is triggered to reawaken at the return of the Doctor. If you'll remember, when Derek Jacobi played the Master he had forgotten until the Doctor reminded him giving him the clues necessary to reawaken himself. This could be a situation like that where Ms. Flood is, essentially, a sleeper agent that was only reawakened by the appearance of Ruby and the influx of time energy her presence caused.
Now, these theories are, of course, overly convoluted and silly, but with the return of Russell T Davies as the lead writer on Doctor Who we can pretty much only expect something like this from him.
Davies is the person who gave us Bad Wolf, like ANY of that made a lick of sense. He gave us the farting Slitheen and their plan to blow up the planet and ride the shockwave through space on an explosion. And is pretty much responsible for every major return of the Master in Doctor Who. Davies is the harbinger of unpredictability in the Doctor Who universe, and as such my theory wouldn't be that much of a stretch.
Of course, with the new season of Doctor Who not starting until spring 2024 and the cast woefully devoid of any easy-to-trick cast members like Marvel's Tom Holland, we are going to have to wait. That said, honestly, I'm familiar with Davies' style and I bet I got this cracked. Let's see.
The fourteenth series of Doctor Who will premiere in May 2024.