Theory:Doctor Who television discontinuity and plot holes/Journey to the Centre of the TARDIS


 * The Eye of Harmony is depicted as a star instead of a black hole, which it had been in every other story in which it was featured.
 * No, it's a star caught at the moment of collapse into a singularity (i.e., a black hole).


 * How exactly does fooling him into thinking he's an Android work? Even without his personal memories, and bionic parts, he would still get hungry, thirsty, tiered or need the toilet. How could they explain these biological attributes if got him to think he was an android.
 * They half did that with the "explanation" they gave the Doctor for him needing the protective suit and respirator - that his "skin" is an organic dermis and needs the same protection as human skin. That could be stretched, but...
 * There are no other androids for him to compare to. So they tell him that he's an android, but it's not like he has experience with other androids to compare. He knows that he's different in some ways, his eyes and his voice, and he takes the rest for granted. If you were told every day of your life that you couldn't be afraid, couldn't feel pain then when you felt something akin to fear or pain you'd think that something was wrong with you, or that you weren't good enough. We don't know that his brothers told him that androids didn't get hungry or have bodily functions. Why would they? And if his brothers never told him that androids didn't need to breathe or eat how would he know any better?
 * If the Time zombies are they're future selves, leaked out of time, when they were trapped in the room by the time zombies. What exactly caused them to become time zombies in the first place?
 * And why were they, post-death, trying to kill themseleves?
 * We don't know exactly what they were "post-death". Did they retain any of their human consciousness? It seems like they retained very little. They seemed to be full of pain and rage and drawn to other humans. We don't know why they were drawn to other humans, they might not have even known themselves. Maybe they recognised a bit of themselves. They were after all drawn to the living versions of themselves in particular.
 * It has something to do with the Eye of Harmony. Think of it in terms of parallel universes:
 * There's a universe in which when the TARDIS was pulled by the magno-grab the remote never fell into the console room. This is a world in which Clara never burned her hand.
 * There's a universe in which when the TARDIS was pulled in by the magno-grab the Doctor at some point retrieved the remote from the Brothers. The remote was outside the Tardis and the Doctor retrieved it and brought it into the Tardis. When the Doctor and Clara got to the center of the TARDIS he was able to throw the button into the Time Crack.
 * There's a universe in which the Doctor, the brother and Clara stayed too long in the room with the Eye of Harmony and turned into the molten-lava like zombies. This can be as many as three separate universes or it could just be one.
 * There's a universe in which when the TARDIS was pulled in by the magno-grab the remote came flying through the Crack in Time. Clara burned her hand. The brothers were turned into molten-lava zombies while fighting time zombies (molten-lava like zombies formed in a different universe bleeding through the cracks in time)
 * There's a universe in which when the TARDIS started being pulled in by the magna-grab a remote fell through the Crack in Time. Clara picked it up and burned her hand. Another Doctor poked his head through the Crack in Time into the TARDIS and warned the Doctor. The Doctor, having heard the warning picked up the remote in time and hit the button.
 * There are probably more universes, but these are the ones we definitively know about. Time is bleeding. We're seeing things that happened, things that will happen, things that could have happened all at once. It's an incomplete time loop. Each repetition is not the same as the last. Incomplete time loops by their nature are very unstable. There are probably hundreds of universes where everyone we saw perished, and perished different ways. But all it takes is one universe where the Doctor manages to prevent the explosion. This happens and the loop ends, stabilised.
 * There are too many "universes" (bad choice of word) there. According to how you've defined the loops one loop doesn't change unless an element from another loop meets it sending it in another direction.
 * Therefore loops 1 and 2 are the same loop, why? Because the remote coming through is the only element that could change the path of time at this point and the Doctor gives this event little head on the first path we saw.
 * The Doctor picked the remote from the brother's pocket because he knew what a magna grab was and was probably looking for it other something similar. It's an investigative strategy he'd be sensible enough to use in all circumstances and in all loops. At the end he sends it through the crack to start the next loop but what circumstances he sent it in are unknown.
 * As for Clara she ends up in the middle of the TARDIS unbranded and, contrary to what she thought later, she opens a door, doesn't move fast enough and is engulfed by a fireball. She dies clawing her fingers into the corridor wall making finger arks her later self is able to put her fingers through. This event is necessary to create the first Clara time zombie, without it there's no reason for anyone to get caught next to the eye of harmony in any loop.
 * The rest could well follow as you suggest but if any others can be merged it might be worth it.
 * The Doctor doesn't need Clara to send the remote back, he does need her branded hand to tell him he's tried and previously failed to send the remote back and thus stop repeating a mistake.
 * Oh, and whatever happens to Clara and the brothers, the Doctor never becomes a time zombie. Such an event would end the loop which can only keep going if the Doctor is able to reach the crack and send the remote through.


 * If keeping his name a secret is so important to him, why does the Doctor have it writen in a big shiney book in the middle of a room that anyone (including rogue salvage operators) could walk in to? Have none of the recent companions ever wanted to do a bit of light reading?
 * I know, right? The Doctor does make it sound like someone would have needed some impetus to go searching the library. Like Clara only looked because something was going wrong. These things maybe were protected some way. But I like to think of it differently. The TARDIS isn't just everything in the world, it's the Doctor's home, which means that their are large parts of the TARDIS that function as a museum or a mausoleum. Those are things the Doctor doesn't like to mention, doesn't like to remember. Maybe that's one of the things driving him. He's running away from the memories that he's carrying around with him. Not just emotionally, but physically. And he keeps his companions busy because he doesn't want them to reflect on certain parts of him.
 * Given what we saw elsewhere in the episode, there's also good reason to believe that, for whatever reason, the TARDIS wanted Clara to read that book and led her to it. One of the most clear things in this otherwise incredibly unclear episode was the TARDIS's ability to lead people around the ship to wherever it wanted them. When she found her way to that echo control room it kept her there for her own safety as, according to the Doctor, it was meant to do. Yet, she found her way to the library first.
 * The TARDIS can also change her configuration at will. Whatever door Clara walked through, even if it were the door to the pool or the wardrobe or the butterfly room last time Clara checked, if the TARDIS wants it to open to the War Museum and Library room this time, it will. And if the TARDIS doesn't want Clara to find that room again later, she won't.
 * Given the events of TV: The Name of the Doctor, we can't be certain that the book wasn't created by the TARDIS herself, or placed there by the Doctor, or one of the Clara fragments. There is nothing in the episode to suggest the Doctor had anything to do with the book. Note Clara is able to find the Doctor's name within seconds of opening the book; she's being manipulated.


 * The real question is: How does this book even exist? Who could possibly have written a History of the Time War except the Doctor, or maybe the Master or Dalek Caan, none of whom seem to have much motivation to do so. (If there's some unknown-to-us other survivor, he's also unknown-to-the-Doctor, which wouldn't be very likely if the Doctor had a copy of his book. Unless the Doctor's memories have been blotted out because his head's full of a backup copy of Gallifrey, but they already did that story in the novels.)
 * As noted above, we have no idea who created this book or when; it might well have been created specifically for Clara to find. The Doctor may not even know of its existence.


 * When the TARDIS, is grabbed by the magnetic tractor beam of a space salvage ship, how come and how does the Doctor end up outside the TARDIS, while Clara is left inside? They were both in the same location (ie the console room) at the time.
 * An explosion happened, and they were thrown in different directions. He likely stumbled/fell out of the TARDIS himself, while Clara was thrown and/or stumbled down a corridor.
 * The way this is visually portrayed makes this physically impossible, and likely is the result of production errors. We see the inside of the TARDIS when it's first grabbed, and then we see it being passed by these big mechanic arms, conveyor belt like before it lands on a pile of junk (where Tricky later sees the Doctor's legs). The brothers watch it being brought in and don't see anyone--it would be kinda obvious if the Doctor was on the outside à la Harkness. And the Doctor would have then had to fall under a pile of junk that the TARDIS was pulled on top of.
 * Or he just climbed out and collapsed after the TARDIS was brought on-board.
 * Another unclear part of the episode, I think we're meant to understand something happened when the TARDIS heart was damaged. Remember that the TARDIS isn't actually a small wooden box it just looks like one, so presumably there are ways out the TARDIS other than the one we imagine the Doctor would have to use.

Somehow the TARDIS internal configuration, whatever makes the infinite dimensions of the TARDIS infinite, failed or changed with the result that when they were restored the Doctor had gone one way and Clara the other.
 * The TARDIS can materialize around an object, and it can also dematerialize around an object, leaving an object that was inside it actually outside it. This was seen in e.g. Blink. It is thus possible that the TARDIS dematerialized around Doctor in such manner to drop him off, and then rematerialized again. Remember that the TARDIS was broken, so any random effect / malfunction could have happened, including such selective and momentary dematerialization.
 * Yes, that's not dissimilar to how I was thinking because how the TARDIS materializes and de-materializes must be connected to how the TARDIS manipulates and moves through its infinite dimensions. Everything that makes the TARDIS what it is and do what it does must be connected. However, in Blink we did, indeed, see the TARDIS de-materialize around its occupants while in this story we watch the TARDIS brought in and never see any sort of de-materialization. Therefore the two processes can't be shown to be exactly the same. Clara ended up far from the control room, the Doctor ended up outside the TARDIS altogether.


 * How does being burned by the Eye of Harmony change the characters' DNA from "human" (or Time Lord, in the Doctor's case) to "animal," but with a "human core element" (whatever that is)?
 * Their DNA is no longer identifiable and so the machine reads out that it is some kind of animal. Some of the human DNA is unaltered though and it's able to read that.