Sorry, that was rubbish. There was no story, just some creepy corridors and then we meet the mother and everything's fixed in two minutes. The entire thing was utterly pointless. The season doesn't seem to be progressing in any way - we've had the same tease about the 'arc' for four episodes in a row now.
I agree that that seems like the obvious answer, which is exactly what makes me think that's not what it is. Moffat deliberately let the Simm Master be seen in the trailer, then he set up this obvious question of "who's in the box?" He knows perfectly well we would put two and two together and assume that the Master is in the Vault, which makes me think that's too obvious, and he's actually playing a deeper game than that. Because if not, then he's basically given the entire mystery away in the trailer and rendered the entire season spoiled, and why would he do that?
Moffat is clever enough to deliberately misdirect us like that. He's done it repeatedly before - let out set photos that show Cybermen so that we wouldn't be thinking about Missy being a female Master. Letting everyone know Missy wasn't dead so that we'd be wondering about that and not be expecting oops! there's Davros. Encourage 'spoilers' that the Clara in the diner was a timeline splinter so that the twist that it's the Doctor who can't remember her would be a surprise.
I can only hope that this is another double bluff here because if it is the Master in that box, even despite all the clues that are rightly being pointed out, then it's just too obvious and we've already figured it all out by episode four.
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