Theory:Doctor Who television discontinuity and plot holes/Deep Breath


 * How could the Eleventh doctor know that he would have another incarnation if he was at 13 and was not granted another set of them yet?
 * The Eleventh Doctor called Clara after he had already received the new cycle from the Time Lords and regenerated partially on the clock tower. He made the call in between blowing up the Dalek ship and giving his "we all change" speech to Clara.
 * The Doctor had aged so looked old when he was on the clock tower and didn't return to looking young again until he was in the Tardis with Clara, about to regenerate, but the Doctor making the phone call looked young. So unless the Doctor went through phases of looking young and then going back to looking old after his regeneration, he couldn't have made the phone call when you said.
 * The Doctor reverted to looking young before Clara entered the TARDIS. Plenty of time for him to have made the phone call, given that she was busy helping get people settled after the fireworks. And the scene very clearly places the call to have occurred exactly then, right before Clara goes to the TARDIS and finds the phone unexpectedly off its hook...


 * How did a giant dinosaur get away without being recorded in any history books or anything? Shame they didn't explain that.
 * "Do you remember the Zygon gambit with the Loch Ness Monster? Or the Yetis in the Underground? Your species has the most amazing capacity for self-deception, matched by only its ingenuity when trying to destroy itself." - Seventh Doctor, Remembrance of the Daleks.
 * As the body was burned to ash, and there were presumably no photo's taken, there is no way to prove it happened. It would probably be dismissed as just another Victorian myth, like Spring Heel Jack.
 * In addition, the Torchwood Institute was already in existence by this time, so they may have had a hand in covering it up.


 * If the TARDIS were inside a dinosaur, then why did it come to the future (or past) with the doctor? Yes, if something is on the TARDIS (CAPTAIN JACK) Utopia (TV story) then it travels with the TARDIS, but if something is touching the base of the TARDIS (buildings, THE DINOSAURS TONGUE) then it doesn't travel with the TARDIS, the TARDIS Would just leave without the thing being brought with it. So, why did the dinosaur come?
 * The TARDIS was crashing after The Time of the Doctor and the Doctor couldn't remember how to fly it. It's not unreasonable to suppose that some ship's setting might have been set up incorrectly, causing it to take the dinosaur with it.
 * The TARDIS did not appear to be resting on the tongue. As the TARDIS was lodged in the dinosaur's throat and was coughed up to expel it, it seems more likely that the contact with the sides of the TARDIS allowed it to be brought along for the ride.
 * The Time of the Doctor confirmed that the TARDIS (who is alive, remember) threw a protective field around Clara when she travelled to Trenzalore on the outside of the TARDIS; presumably, she extended the same courtesy to the dinosaur.


 * There is an obvious hair continuity error for the Doctor between The Time of The Doctor and Deep Breath. How did his hair get so short after being much longer and curly?
 * Since regeneration energy lingers around for a while after a regeneration (as seen in The Christmas Invasion and Let's Kill Hitler for example) it may have taken a bit longer for his body to settle on a final appearance.
 * We also don't know exactly how long it was between the two scenes. While it's unlikely they stopped off at a barber, given how manic the new Doctor is, who is to say he didn't do something to shorten his hair? Also, sweat and getting wet can also make it appear shorter.


 * Why would wearing a face/mask be an effective way for the doctor to disguise as a robot? He is just as much in view as Clara, and he still needs to breathe!
 * The droids were likely paying attention to Clara, who was doing all the talking.
 * Actually he doesn't. Time Lords can hold their breath for a lot longer than humans, and the Doctor has shown in the past he can survive for periods of time without breathing.


 * How did the Paternoster gang get into their ambush position in the roof of a spaceship, deep underground?
 * We don't see much of the roof in any great detail. There may have been a vent.


 * Why would Strax have any difficulty dispatching a few non-combat-specialised robots, even unarmed? It's difficult to reconcile this cowering, weak character with the 10th Doctor's admonishment that "You can't fight Sontarans!"
 * Strax gene-splicing himself for nursing purposes may have imposed some kind of hindrance. Alternatively, he may have lost some of his combat skills when Vasta and Jenny brought him back to life after Demon's Run. In The Snowmen, the Doctor does say that he's not sure all of Strax's brains made the return trip.
 * Additionally, Strax does note that the droids won't "stay dead". Presumably, as he's damaging them, they keep self-repairing and continuing to fight.


 * What could be the explanation for the gigantically huge Tyrannosaurus Rex dinosaur? Or any possible hints as to what sort of backstory could entail such a radically huge creature? Or why no one would mention that it was over ten times bigger than any recorded specimen?
 * It's the policy of this wiki that the DWU is treated differently than the real world. There's nothing that says a dinosaur that huge cannot exist in the DWU.
 * And, indeed, even in the real world scientists keep discovering previously unknown dinosaur species, and more than a few in the past have also had their estimated size revised upwards and downwards.
 * But look at the T-Rex in Invasion of the Dinosaurs - it was much, much smaller!
 * Jenny and Vastra have a discussion about it. Jenny says dinosaurs were much smaller, but Vastra (who actually lived in the same time period as they did, and is presumed to have much more accurate knowledge) says that actually *most* of them were about that size.
 * Besides, when do they say this one is a T-Rex?


 * The T-Rex is seen in one shot right next to Big Ben it's head level to the clock face. This is impossible as Big Ben is 315ft tall and no dinosaur was ever that long let alone that tall.
 * Actually, look at the Classic Who story, Planet of Giants (TV story); In that serial, the TARDIS doors open in flight, and the resultant exposure to the time energy caused the occupants to shrink. It isn't that much of a stretch to guess a similar effect happened to the Dinosaur.
 * All of the above explanations are valid responses. In addition, they did address this question in the episode itself. Jenny says she's seen fossils of dinosaurs, and they were much smaller. Vastra corrects her that she actually lived at the same time as dinosaurs, and says most of them were actually that size. (Again, this is in the Doctor Who Universe we're talking, not necessarily reality.)


 * Where are Torchwood members? A time-travelled-Tyrannosaurus has just vomited a blue box with 'police box' written on it. Surely they should have guessed it might be the Doctor.
 * Hmm, good thought. I guess it depends how concerned Torchwood are about keeping on the DL. They might also have thought that if the Paternosters were dealing with the dinosaur business, they're best off keeping out of their way (compare not getting in UNIT's business during the 1970s).
 * Weren't Torchwood only after the Tenth Doctor? Even if they were able to find the TARDIS, they may have kept an eye on them and seen it wasn't him. Cause they probably weren't aware of regeneration.
 * According to on-screen evidence, Torchwood wasn't properly organised until the late 1890s and at the time was a very ad hoc organisation with just a few members. Deep Breath and the Paternoster stories appear to take place circa 1892-1893, several years earlier. Torchwood existed, but may not have been in any shape to do anything at this point; it didn't seem to ramp up until after recruiting Captain Jack (who at this point in time would be avoiding encountering any Doctor who wasn't the Ninth or Tenth per "Utopia") and may not even have been in England.
 * It's actually quite possible in retrospect that events such as the dinosaur in the Thames could well have inspired the acceleration of Torchwood's development. Plus, the nature of Vastra's relationship with Torchwood (a humanoid reptile female would not go unnoticed by everyone especially if she keeps unveiling herself in public as she does in this episode) has never been established.


 * Although all eyes were likely on the dinosaur, it's still odd that Vastra would unveil in front of a large group of people (at one point raising her voice to her colleagues, hence potentially calling attention to herself).
 * Perhaps, but presumably she was indeed relying on the general crowd being focused on the dinosaur and their resultant fear of it.
 * It's also possible that by this point in time (we don't know how much time has elapsed for Vastra since The Crimson Horror) people may simply be familiar with the "oddly disfigured" woman, though this is somewhat contradicted by Vastra's later veil speech to Clara, though the validity of said speech is questionable after it is revealed to be a test.


 * At the end "the Girl in the Fireplace" Rose asks the Doctor why the androids were going after Madame de Pompadour. The Doctor says he doesn't know and the final shot shows the name of the spacecraft (SS Madame de Pompadour) as the Tardis dematerialises. As the Doctor never knew the name of the SS Madame de Pompadour, how can he know that the SS Marie Antoinette is its sister ship.
 * It says so on the bottom of the phial.


 * When Clara last left her own time period in The Time of the Doctor, it was Christmas Day. After being on Trenzalore, and then in 1890s London, the Doctor brings her back to the 21st century...in Glasgow, at a time that is clearly not Christmas day (or anywhere near the Christmas season by the looks of it). In Glasgow, the Doctor leaves Clara to go get coffee for them, and that’s apparently the last time Clara see’s him until Into the Dalek, set weeks later. All of this implies not only that Clara basically went missing for a few days or weeks on Christmas Day (she ran out of flat and never came back, as far as her family know), but that the Doctor then went and left her completely stranded in Scotland.
 * Her family last heard her having a break up with her "boyfriend" and then running off. Once she returned, she could of brushed the whole thing off as her running after him, and spending some time with him until they broke up again and she returned. She's back at Coal Hill by the time of Into the Dalek, so it can't be any further than the time of the Winter Term that she came back.
 * Regardless, she'd have to have been gone for a while with no word to her family, which surely would've got her registered as a missing person.