Theory:Doctor Who television discontinuity and plot holes/The Power of Three


 * Brian stays in the TARDIS for four days watching the cubes, without noticing that it has been four days. Does he not feel hungry or tired during that period of time? Furthermore, it's implied that he's just been sitting there for four days without realising how much time has passed, humans can only survive for three days without water, and even the most patient of people would realise the time they've been sitting somewhere staring at cubes.
 * It has been previously stated in many episodes that time doesn't pass the same way in the TARDIS than outside of the TARDIS, so for him it could have been only a few hours.
 * Plus anyone who has been immersed in videogames or other activities can relate how easy it can be for time to pass without realizing.


 * If the Doctor, Rory and Amy were able to jump through the portal as it exploded, surely parts of the explosion itself would also travel through?
 * Not necessarily, it depends how the portal works (for example, may be keyed only to work on living beings).
 * In that case, how do the strechers and there clothes also make it through?
 * The moment the explosion went of, the portal's power source would have been destroyed, so the portal would have closed,thus nothing could have got through


 * If the cubes could scan all information on people, then what was the point of kidnapping the humans?
 * Remove key witnesses? But doesn't stack with old man's removal.
 * Learning more about people for the eventual purpouse of destroying them.


 * Who were the aliens with large mouths and what happened to them?
 * Servo-droids to keep the little girl safe? They were on patrol back on earth probably when Doctor and Amy T-ed.


 * In this story electricity effects the doctor like a human, but in several other stories (Terror of the Zygons, World War Three, A Christmas Invasion, The Pandorica Opens etc) he's shown an incredible resilience to electricity.
 * That's never been very consistent. For example, we've seen him be afraid of, or at least wary of, electric bolts from Rutans (Fang Rock, Gunpowder Plot) and the Master (The End of Time).
 * There are a great many different types of energy; some of them affect him very little, some of them affect him a lot. For example, the Master in EoT was using the raw energy of his life force. That's got to be more potent to a Time Lord than a lot of other energy!
 * I dont' remember if it was ever said on screen, but in Confidential they called the Master's energy "electric bolts" over and over again. And Rutans are definitely electric. And there aren't different types of electricity.
 * Tell that to Terry Nation, Kit Pedler, and various other early writers, who clearly seemed to think static electricity was some kind of magic… :)


 * When removing the cubes from the hospital, no one seems to notice the little girl still has one.
 * Presumably people are cooperating with the staff, and they're in a big hurry, so they may not have noticed if she did anything at all to hide it.


 * Surely someone would have noticed the fact that the same girl was in the hospital for a year.
 * Most likely she hides and/or comes &goes.
 * It could also be that she has some sort of perception filter.


 * Why does no one notice the disappearing patients?
 * They very well may have noticed some of the disappearances. They still wouldn't have found them.


 * In this story having only one heart is impossible for a timelord to manage, but in the past he's survived with only one heart.
 * He survives this time too. It's not impossible to manage, it just leaves him weaker than usual. The last time he was down to one heart, in The Shakespeare Code, he was weakened, and couldn't chase after the Carrionites until Martha helped him restart the other one. And, unless you believe that the First Doctor had only one heart, this has been consistent throughout the series (and the novels—see the whole Sabbath storyline). Even non-Gallifreyans with two hearts explain that people with one heart are much weaker (e.g., The Dominators).


 * How does the visual aid recognise the doctor?
 * Why wouldn't it?
 * This might be a reference to the background arc of the Doctor erasing himself from history. Perhaps he missed a spot.


 * After the spaceship exploded, only Amy, Rory and the Doctor escaped. What happened to the people inside?
 * They may have gotten some or all of the people out before the confrontation with the hologram. Anyone they didn't get out died. That's not a discontinuity; people die in Doctor Who.


 * It is stated that the boxes only affect 'human' hearts, yet one of The Doctors hearts is damaged by them. Are we to question whether The Doctor does, in fact, have a human heart, thereby giving credence to the idea that he may be half human? Any ideas?
 * Maybe it only affects human-ish hearts, excluding the non-humanlike second heart of the Timelord? This being the 21st century and before humanity's official first contact with aliens, it might have been safe for the Shakri to assume that their device would only be used on humans.
 * Given that another revelation of the TV movie - the presence of the Eye of Harmony within the TARDIS instead of on Gallifrey - is affirmed in TV: Journey to the Centre of the TARDIS, it is possible that this is a subtle affirmation of the "Doctor is half-human" revelation from the movie.