Theory:Doctor Who television discontinuity and plot holes/Forest of the Dead


 * It is never explained how the Doctor got out of the handcuffs as it was shown that he couldn't reach the sonic screwdriver and there is no evidence that anyone freed him.
 * It's likely Donna got him out of the handcuffs, also, this might not count as an error, just simply never explained. Also it has been proven that The Doctor has met Houdini.
 * He couldn't reach the two screwdrivers with his hands, but he could have tugged them closer with his feet.


 * If the Vashta Nerada are now living on the planet, does that not mean that CAL and its hardrive will be destroyed?
 * Vashta Nerada only eat meat. The hardrive is not edible and therefore not threatened.


 * During the scene when everything goes white, when Lee bursts through the door - he shouts Donna! But Lee could not say her name properly because he had a stammer.
 * Stammers are often not constant but rather caused by stress - there were several scenes in which he spoke without the stammer.


 * The future Doctor apparently places one of the communicator links in the sonic screwdriver to save River's mind, yet the suit she is wearing when she dies also has one of the links.


 * It is unknown if the communicator on her suit was intact after her death. If the transfer fried her brain, it may also have fried the communicator, which mirrors her brain activity.


 * Also, from a story point of view, it's more dramatic for the communicator to be in something that is easily portable, which can make for a nice running sequence to complete the upload.


 * How were the data ghosts of the crew transferred from their suits' communicators into the computer when the Doctor had to plug River's screwdriver physically in to transfer her? Why couldn't the computer just read the screwdriver's communicator remotely, the way it apparently did the suits'? Via the Library Wifi.


 * How has River carried the sonic screwdriver for as long as she has and never once noticed that a bit of it just slides right off to reveal a communicator link? (If she had noticed, apparently she didn't think it was worth telling the Doctor about.)


 * Given that the Doctor and River keep encountering each other out of order, how would the Doctor have known what was to be River's next-to-last meeting with him before the one that led to her death, in order to be all moody about it and to give her the sonic screwdriver? It could be their very next encounter, or could take place years or decades into the future of the Doctor's personal timeline.


 * If we assume that River cannot time travel herself, then her timeline is traveling at a normal human pace. The Doctor knows the date that she will go to the library and he knows what would happen to her. He can only cross paths with her so many times before he runs out of chances (she's only, what, 40 years old?), so when it's no longer possible for him to meet with her in her timeline, he gives her the screwdriver.


 * However, based on later seasons, River can time travel herself. She specifically identifies herself as a time traveler who keeps meeting the Doctor out of order.


 * There is never any sign of Anita being eaten and the green light on her communicator never flickers. However, when Proper Dave was eaten he spasmed horrifically and the green light on his communicator eventually went out.
 * By this point, the Vashta Nerada are trying to conceal that they have eaten her, as they hope to convince the Doctor he is still talking to Anita.


 * When the shadows are stretching from Anita to the Doctor, the shadows of the equipment move away.
 * These shadows have Vashta Nerada in them, and they are moving as well.


 * How come the Data Ghosts in the system didn't get transferred out? CAL brought the crew of Mr. Lux's expedition back through the computer not their Data Ghosts. It is possible that the Vashta Nerada Data Ghosts did not get uploaded but the Miss Evangelista disfigured Data Ghost should still have been brought back out (downloaded).
 * The 4022 people in the system were alive when teleported into the system. The crew's Data Ghosts were indeed captured by the system and downloaded into the system. But as they have no physical body outside the computer they can only exist inside.


 * After the people have been teleported back into the library, Strackman Lux says "4,022 people saved!". However, including Donna, there were actually 4,023 people.
 * He was probably just referencing what had been echoed in the entire episode.


 * Why would the Doctor need years to think of a way to save River when he already knows?
 * It undoubtedly took time to refine the neural chip and other advancements to his screwdriver so that it only stores River's consciousness. -Besides, he was only commenting how his future self would have had a timeframe of several years to figure something out, not that it actually took that long. The current Doctor would have no way of knowing how long a solution will actually take, just that his future self would have years to work on it before it was needed. Considering that he now knows what he did to save her, it'll probably take him no time at all to rig it up when the time comes that he needs to.


 * If nothing can get through the TARDIS forcefield system when she appears in the TARDIS how did Donna get eaten and put on a parallel world? The Doctor sent her there, so that leaves us with two possibilities. Either A) he overrode the security protocols before sending her in or had them down in case he needed such an event or B) teleporting into the TARDIS is possible. Given that the Emperor's Daleks have done, Donna did it (albeit due to a special particle infused in her bloodstream), and other rather bizzare events, there's strong enough evidence to suggest that it's possible given some forms of technology or users. Nor is there a reason to assume that nothing can get into the TARDIS because it has a forcefield, rare as it is.
 * The TARDIS' defensive systems don't stop teleportation (or only do so erratically, as per most of the systems), instead simply signalling the Doctor about a breach in the TARDIS. The reason Donna was taken into CAL's world is because CAL intercepted the teleportation and "saved" her, like the survivors.


 * Lee is an individual of the far-future, and the Hardrive can take anyone who was loaded into it in any era of their chose. When Lee and Donna get married and have children, their life is set in Donna's era, wouldn't Lee have a problem coping such a primitive time.
 * It is stated that CAL could live in any era. She appears to be stuck living in the 21st century, along with all other saved people, while she is in her amnesiac state. Everyone, like her, would have their mind adjusted to fit into this era (with help from Doctor Moon).


 * Why do the Vashta Nerada let the Humans go? With the planet sealed off and no prey available, won't they eventually starve to death?
 * It's possible that there is still some form of life on the planet. The Nerada seemed more angry about their presence than they did their overall status as food. It's worth pointing out that they had survived sometime before the Doctor had arrived and the people were already gone for some time. The Doctor also managed to reason with it, so it is intelligent, so there's no reason to assume that they're heartless killers, acting more out of fear of humanoids rather than a desire to devour them (ie, they're a scavanger race, the Doctor says that they're on many planets, including Earth).


 * The "Donna" exclamation the Doctor makes when he briefly makes contact with the virtual world is in a higher pitch from Donna's point of view, but in a lower one from his.
 * Many forms of communication include pitch distortion.


 * River: "Some days, nobody dies at all. Now and then, every once in a very long while, every day in a million days, when the wind stands fair and the Doctor comes to call...everybody lives." Yeah, for some value of "lives" that encompasses "has all the flesh stripped from their skeletons and then has their brains uploaded into a computer on a planet infested with flesh-scavenging shadows which no human will ever come to visit again. Where they then get to stay, just the half-dozen or so of them...forever." That's a real happy ending, that is.
 * If you listen to Ray Kurzweil, the Transhuman Foundation, the Extropy Institute, Humanity+, etc., uploading into computers to live forever is pretty much the ultimate happy ending.
 * Of course if you listen to those same people, you have to ask why all of humanity wasn't uploaded by the late 21st century; the fact that they weren't might imply that the extropian/extropist/transhuman community turned out to be wrong....


 * In A Good Man Goes to War, River is revealed to be Melody Pond, a human with traces of Time Lord DNA due to her being conceived in the TARDIS during flight in the vortex and it is implied that she is the little girl who regenerates at the end of Day of the Moon is seen to regenerate. If River can regenerate why doesn't she do so at the end of Forest of the Dead?
 * Maybe she did? We don't see what happens to her body after she "dies". She could have   regenerated without the Doctor's knowledge.


 * If interfacing with the core would have killed the Doctor it presumably would have killed River Song as well.