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So, in the final episode of series 9, the Doctor is without his TARDIS, it having been left in London during a previous episode.

Not mentioning the beautiful art that Rigsy did to his TARDIS, (which we'll save for another question about whether the Doctor realized who it portrayed (Clara)) —

How did Clara and Me transport the Doctor’s TARDIS using their own? Shouldn't this have been a disaster? If we look at the mini-episode Time Crash when the 5th and the 10th Doctors’ TARDISes crash into each other, it doesn't bode well.

How then was Clara able to transport the Doctor’s TARDIS to the desert?

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The Doctor has in the past landed his tardis over the Masters tardis without major issues and transported it. They also at one point each tardis was inside the other like an infinite hall of mirrors, the difference is in the mini episode, they crashed together – ATB Jan 19 at 10:42
up vote 5 down vote accepted

The diner TARDIS is unique in that the door to the control room doesn't open to the immediate outside but rather into the diner-counter room. There are 2 possibilities.

A

The diner room is not actually "inside" the TARDIS but part of the illusion of the outer shell. If this is correct then there is no need to presume the Doctor's TARDIS was inside Clara's TARDIS. Clara could easily have arranged for it to have been shipped from the UK to the US.

B

The diner room is actually "inside" the TADIS in which case it would appear that Doctor's TARDIS was inside Clara's TARDIS. There have been a few instances of "one TARDIS inside another/same TARDIS" but they have always been considered at least risky behavior if not a serious emergency. It is possible that it's only a problem when it is unplanned (as seems to cover all the previous cases) but it's safe when it's planned especially if done with the explicit co-operation of the Doctor's TARDIS.

In either case it's clear that the TARDIS appeared to be only a few feet away from where he was standing in the diner. So either it was hidden from his view or it arrived there, very quietly, just after the diner-TARDIS left. Note that the Doctor spends a few seconds looking around NOT in the direction of the TARDIS until he finally turns all the way around and sees it.

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This is also a good answer which deals with all possibilities. – Evil Angel Jan 19 at 23:03
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it will be interesting to find out what happens to someone in the diner-counter room whilst the diner-TARDIS is in flight in the vortex. We catch a glimpse of it at the end in the vortex and it's external shape is still a diner so presumably the diner-counter room is still there ! – John McNamara Jan 19 at 23:35
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I though the early Doctor-TARDIS designs had a console room door that didn't actually open directly to the exterior, but I can't find any evidence of that now. – Lightness Races in Orbit Jan 20 at 10:48
    
@LightnessRacesinOrbit I remember that too, I think it had something to do with the fact that they couldn't do the inside-outside visual effects well enough iirc... – BMWurm Jan 25 at 20:44
    
I think they were just very careful to never show a clear direct line of sight through the door when it was open, from either side, to keep production costs down. Obviously not a problem on the modern show. – John McNamara Jan 25 at 20:54

Yes, The Doctor's TARDIS was inside the Clara's TARDIS and it's not the first time it happened. Time Crash shows a different thing (i.e. Crash of the same TARDIS from different time). It's not landing one TARDIS into another. Here are some previous incidents in which one TARDIS landed into another:

  • In The Doctor's Wife episode of new Doctor Who (2005), The Doctor landed a (Proto-)TARDIS (which he built himself) inside his original TARDIS.

  • In Logopolis episode of the original Doctor Who, The Master and The Doctor's TARDISes landed inside each other.

If that wasn't enough, The Doctor's TARDIS has landed inside itself creating huge paradox of both Time and Space (Watch mini-episodes Space and Time).

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While the Logopolis incident lead to infinite recursion, it was never stated whether this was disastrous or an just amusing/confusing accident. – OrangeDog Jan 19 at 16:51

As you say, Time Crash had the 5th and 10th Doctors’ TARDISes crash into each other.

That’s presumably different from, and much worse than, one TARDIS materialising around another TARDIS, which I’d guess is how Clara and Me managed to transport the Doctor’s TARDIS from London to the desert.

I think this is plausible — in our universe, there’s a difference between, for example, a car going inside a truck:

enter image description here

And a car crashing into a truck:

enter image description here

I think it’s also significant that the 5th Doctor’s TARDIS and the 10th Doctor’s TARDIS are the same TARDIS at different points in its time stream. My puny human brain can’t begin to work out what sort of paradoxes that might introduce.

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But, if TARDIS's could just materialise around each other, then why hasn't Missy just used that to find the Doctor when he went missing? And love the crash difference :) – Mafalda Hopkirk Jan 19 at 10:44
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You need to know where the Tardis is. And generally I think they're shielded to prevent it – ATB Jan 19 at 10:53
    
@MafaldaHopkirk Has Missy had the use of a TARDIS? I remember one of those wristband thingies. I don’t remember her with her own TARDIS. – Paul D. Waite Jan 19 at 11:08
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@PaulD.Waite Yes. The doctor, and though I struggle to remember the episode, I believe the penultimate on series 8, the Doctor explicitly says "She must have a TARDIS somewhere". Although it is intriguing that she uses the Vortex Manipulator in the newest series. – Mafalda Hopkirk Jan 19 at 11:11
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+1 for Knight Rider – Lightness Races in Orbit Jan 20 at 10:49

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