Theory:Doctor Who television discontinuity and plot holes/The Almost People

Madame Kovarian is from the 39th Century so Flesh technology is probably common by then.
 * How could Madame Kovarian acquire the flesh technology?


 * Does The Doctor now know about his death? Towards the end the ganger Doctor says "this is my death i suppose" or words to that effect, to which the real Doctor replies "only this time we're not invited". The Doctor appears to know about his death after Amy told the Doctor she had seen it, in the scene where Ganger Doctor talks about the eyes asking "why?" when gangers are "executed". How does the real Doctor know about his death? If the shoes were already swapped at this point then this would explain it, however The supposedly ganger Doctor then gets angry at Amy due to sensing the flesh wanting revenge, the supposedly real doctor feels the same but not as strongly, so have they infact not swapped at this point? This would mean the ganger Doctor would ahve to have told the real Doctor what Amy had said.
 * The Doctor was trying to see if Amy treated him and the ganger differently so his outburst could just have been an act to convince her he was the ganger. Presumably they swapped shoes very early on.
 * The original Doctor does seem to have been the one Amy told about his death. In the Ganger Doctor's final moments with the real Doctor, the former talks about his death and the latter comments about it not being one he was "invited to". His earlier outburst could have been to continue the ruse that he was a Ganger being influenced by the Flesh, or he genuinely felt something about Amy not telling him before but being willing to tell his Ganger just so he could sacrifice himself for the 'real' Doctor. After all, he was trying to make a point about both Doctors being equal.


 * The Doctors appear to be sharing the one sonic screwdriver in all of their scenes together. But when Doctor #1 is knocked unconscious, and Doctor #2 is locked in the acid room, they both have screwdrivers.
 * We have seen the Tardis "create" a new screwdriver from the console in the eleventh hour, perhaps this happened during the cut between scenes
 * When the Ganger Doctor was created, so were a copy of his clothes and perhaps the screwdriver.
 * No, because the 'real' Doctor threw his Ganger the screwdriver at the end
 * The Doctor has two screwdrivers? The shark-bitten one from "A Christmas Carol" which has been fixed, and a brand new one.
 * No, the shark bitten one stayed in the shark. The TARDIS has the ability to make new screwdrivers, but neither Doctor had access to the TARDIS until a lot later on.
 * Just because they do share the Sonic Screwdriver, and that's what we see, doesn't mean another one wasn't created.
 * The Doctors are also seen to pass the screwdriver between one another when they are repairing the tracking console.
 * We don't have 100% proof to say that the half inside the shark was there by the end, but it seems likely. I believe when the Doctor was copied the screwdriver was also copied, and they just happened to be sharing the same one because they could, assuming they were actually sharing and one wasn't just fiddling with the other's briefly for some reason. By the end, both screwdrivers would have returned to their owners.
 * There are two Sonics. The Ganger Doctor had duplicates of everything the real Doctor had on him when it copied him. He gave the flesh Sonic back to him during the final escape.
 * There can't be any unseen scene where the Doctor creates a second sonic because the TARDIS is stuck in the ground for this entire sequence of events. Any sonics had to already be on the real Doctor's person from the start or be duplicated by the Flesh. Duplicated sonics doesn't really solve the issue either as it just leads to some confusing scenes. This is what we saw: Ganger Doctor threw a sonic to real Doctor, they then each use a sonic on their respective missions (real Doctor's sonic usage actually having a purpose, Ganger Doctor's not being important to the story), then at the end real Doctor throws a sonic to Ganger. Either Doctor had two sonics with him initially (a spare on the off-chance he would be duplicated by the Flesh he was investigating and it wouldn't duplicate his sonic?), and somehow they both end up in Ganger Doctor's possession so he can throw one to the real Doctor while keeping one himself. That really doesn't make sense, especially since at the end the real Doctor returns the second sonic to Ganger Doctor. So what if the sonic was duplicated? That makes a little more sense that Ganger Doctor ends up with both before returning one to real Doctor; they could have been furthering their switch deceit by pretending they only had one between them, to give the point of 'real' Doctor's absolute trust in 'Ganger' Doctor more emphasis. But that still doesn't explain why real Doctor returns the second sonic to Ganger Doctor at the end! So none of the solutions presented so far work. I've got two possible solutions that I think take into account everything we saw: The most likely is that the script only ever called for one sonic, but Matt Smith never bothered emptying his pockets between scenes. The only scene with a 'second' sonic is when Ganger Doctor briefly analyses the acid to say it is overheating. My guess is that Matt regularly improvises sonic usage in Doctor Who scenes like this one and with the scenes shot out of order everyone just forgot he didn't 'have it' in that particular scene, until it was edited and was too late or expensive for a reshoot. Most likely, but boring!! FANFIC TIME! The episode played out the same, Ganger Doctor dies heroically saving everyone, real Doctor leaves with everyone in the TARDIS. A second sonic is grown and then used to dissolve Ganger Amy. "We will save you Amy! I had to destroy your Ganger body, but that isn't what is important. If only I could have saved that good looking chap... WAIT! His body isn't important!" The Doctor modifies his sonic and travels back in time to just after he and Ganger Doctor initially parted ways and gives his sonic to his sonic-less Ganger self (avoiding crossing time streams by not actually visiting his past self). The episode plays out as seen with Ganger Doctor backing up his analyses of the acid heating with sonic evidence. He dies heroically saving everyone else, a little confused why he had just been thrown a second sonic. The future real Doctor returns to the scene after the explosion, picking up his modified sonic and returns to the TARDIS. A little later Ganger Doctor finds himself alive, on the lawns of a manor, an older River Song running to greet him. He wonders to himself, how long will it take real Doctor to get Flesh to the Library. Solved! That must be what happened! If there are two Doctors and two Rivers next episode you now know why. I can't wait for the episode where the two Doctors find another vat of Flesh and an old astronaut suit, invite their friends' past selves to a picnic and pull the ulitmate prank!
 * The doctor gave ganger doctor his screwdriver but later they both had screwdrivers. Further on the doctor gave ganger doctor another screwdriver! Why?
 * lets just keep things simple like the writers probably intended. the sonic got duplicated, just like everything else attached to the doctor when he scanned the flesh.  they threw the sonics arround to disguise the fact that they had two.  at the end, the doctor throws the real sonic to the ganger doctor, who then got dissolved.  the real doctor then brought the flesh sonic into the tardis, where it stablised and then he keeps using it for the rest of the episode/season.  he may have gone back off-screen to retrieve his sonic between episodes 6/7 while checking if there was any possibility his ganger had survived and could be recruited, but it doesn't matter if he didn't.  all that matters in the end is that the sonic was duplicated and the real doctor used a stabilised flesh one later.
 * lets just keep things simple like the writers probably intended. the sonic got duplicated, just like everything else attached to the doctor when he scanned the flesh.  they threw the sonics arround to disguise the fact that they had two.  at the end, the doctor throws the real sonic to the ganger doctor, who then got dissolved.  the real doctor then brought the flesh sonic into the tardis, where it stablised and then he keeps using it for the rest of the episode/season.  he may have gone back off-screen to retrieve his sonic between episodes 6/7 while checking if there was any possibility his ganger had survived and could be recruited, but it doesn't matter if he didn't.  all that matters in the end is that the sonic was duplicated and the real doctor used a stabilised flesh one later.


 * IIUC... the Flesh duplicated the Doctor, clothes and all, from the last time it "read" him. So, when the start work on the comm console there is a sonic screwdriver and a Ganger sonic screwdriver. I've got a feeling that they juggled it so that everyone thought there was only on and the Ganger Doctor, posing as the original, wound up with both. One, likely the original, was given back to the "Ganger" Doctor for the search for Rory. Hence both Doctors have one during the bulk of the episode. When leaving the acid mine, the Doctor likely gives the Ganger Doctor the original and leaves with none. The reasoning would be that the original would definitely destabilize the Flesh while the Ganger sonic screwdriver might destroy itself before affecting Ganger Jennifer. The sonic screwdriver at the end would be a new one picked up off screen after the TARDIS left the island but before the final scene.


 * If the doctor sterilized the flesh, why was Amy still flesh at the end?
 * You mean "stabilized"? I think the difference is that the other Gangers were independent, while Amy's was still controlled by the real Amy. Whether that meant she automatically didn't stabilize, or that the Doctor left her out of the stabilization field, I don't know.
 * Amy's flesh wasn't sentient as the others had been. She was still connected to it. Thus, it couldn't become human by the Tardis.
 * The Doctor switches shoes with his Ganger. However when he uses his sonic screwdriver to melt the Ganger Amy his shoes do not melt.


 * What's the Jennifer chronology? Clearly the "real" one was the one in the courtyard by the flesh pile, but when and how did these duplicates arise exactly? Is the Ganger leader / sad story-telling Jen the same as the quadruped monster? (Does it matter?)
 * If I got it right... Jennifer lashed up and created Jennifer Ganger prior to the solar tsunami in "Rebel Flesh". The Doctor et al met and interacted with Jennifer Ganger throughout the remainder of that episode and this. At some point Jennifer Ganger murdered Jennifer, likely just be for the Doctor discovers her body. When Rory is following Jennifer Ganger, she set him up by losing him long enough to "birth" Jennifer Ganger 2. The inference is that Jennifer Ganger 2 is the one thrown into the acid pool resulting in Rory believing that Jennifer Ganger is the original. Jennifer Ganger is thus the one that becomes the Ganger monster in the end,


 * When the Ganger doctor uses the Sonic Screwdriver to melt himself, Ganger Miranda Cleaves and Ganger Jennifer, why does Miranda's acid suit melt as well? It was not part of the flesh.
 * Maybe it was part of flesh, cleaves could've touched flesh when wearing acid suit.
 * Unlikely as there were no acid leaks then.
 * Maybe so, but we don't know when they duplicated themselves
 * The Gangers were seen without acid suits and they stole their suits so they weren't part of the Flesh.


 * Assuming the clothes Amy was wearing weren't flesh, they shouldn't have melted either.


 * If Pond has been substituted by Flesh from the season start, there is a complication due to Neil Geiman's episode being out of the universe and very likely unreachable for technology of Flesh control. After all, it is out of time and space of our continuum.
 * No one knows exactly how the technology behind the Flesh works. Bearing in mind that Flesh Amy is a more advanced version of the Flesh seen in episodes 5 and 6, it is entirely resonable to assume that Flesh Amy can be controled outside of the universe.
 * The thing is: enemies, obviosly, have some sort of time technology. And they can send some sort of controlling signal through time. But to reach the House, doctor had to do the usual 'destroy a part of tardis' thing, which is believed to be (as the tardis techonology in its fullness) in Whouniverse unreachable for any enemies other than TLs and Daleks. So, basically, transmitting signal in time (i suppose this is ONLY signal - it looks like transmitting signals through time is not very 'hard' technology - hence all magic cellphones and such) is perfectly fine, but to transmit the signal out of universe you need the technology similar to TLs (Rassilon-level?) and the enemies do not look SO powerful (they have PLAN, no POWER), being stationed in 52 century and such.
 * There is also a possibility that the Flesh 2.0 has a short term "image buffer" that the sonic screwdriver crash along with blocking the primary carrier wave. Remember, "The Doctor's Wife" is the only episode not to include a peep in by Kovarian. A buffer would explain Ganger Amy not dissolving while the carrier wave was "missing" and Kovarian not being able to "look in".


 * If the Doctor believes that the Gangers can co-exist with humans, why does he kill the Amy Ganger? It seems to go against his message during this episode.
 * Because she wasn't made self-aware like the others, she was basically a vehicle for the real Amy.

But 4 humans and 3 Gangers (5 Including the Jennifer Gangers) died! How is that a happy ending?