The new series has established definitively that history can be and has been rewritten; the "cracks in time" in the first Matt Smith season were implied to have erased the events of "The Stolen Earth/Journey's End" and "The Next Doctor" from recorded history.
Although Moffat was ambiguous about the nature of the universe's "reboot" in "The Big Bang." So while apparently the events of "The Next Doctor" and the 2009 Dalek Invasion were erased from history
during Series Five -- which itself seems to have taken place more or less in an alternate timeline from that in which Series Six and later seasons take place, given the effects of the Cracks -- it is entirely possible that the reboot restored the 2009 Dalek Invasion. Or not -- it's never been established one way or the other.
But hopefully not "The Next Doctor." That episode was just rubbish.
(UNIT's overthrow of the UK government in Children of Earth is a fairly obvious possible forking point - a massive demonstration of UN power in the Who-universe, or alternatively a reason for its constituent nations to decide the UN is too big for its boots and reform it into the WZO).
Side-note: UNIT did not overthrow the U.K. government in
Torchwood: Children of Earth. UNIT was pretty much on the sidelines -- collaborating but not taking leadership. The general who essentially intimidated Prime Minister Brian Greene into obeying his commands and ordering the British Army to abduct 10% of the children of Great Britain was explicitly stated to be representing the United States, not UNIT.
"The Name of the Doctor" used a lot of archive footage and characters referenced past adventures of the Doctor, both classic and new. So most of the classic series has to remain intact or has happened in some fashion in spite of all the timeline changes the Doctor has effected or witnessed.
Also, Jo remembered the Doctor and the Time Lords when she met the Eleventh Doctor in
Death of the Doctor over on
The Sarah Jane Adventures -- post-"The Big Bang."
and decide once and for all if the Cybus Cybermen did in fact join forces with the Mondasian Cybermen.
I see no particular reason to assume that the Cybus Cybermen have ever been encountered post-"The Next Doctor." I tend to assume that the Cybermen encountered in "The Pandorica Opens," "Closing Time," "Nightmare in Silver," and "The Time of the Doctor" were all Mondasian Cybermen who happened to look like Cybus Cybermen.
However, the archive footage in Day of the Doctor is used in a different context, showing him rushing to save Gallifrey rather than tracking down Arthur's signal, or following the alien pod to World War II London, etc etc, which would argue towards the idea that the Doctor's past may also be changing as history is changed...
One of the interesting things about "The Day of the Doctor" is that there's no way to know if the Doctor's past has
changed -- i.e., he originally did burn Gallifrey and now he's changed his past -- or if he has only gained more accurate knowledge about his past. Either model works.
In terms of the continuity of Doctor Who, I wondering how many of the earlier Doctor's adventures are still a valid part of Doctor Who's admittedly tangled timeline.
I was watching "Enemy of the World" recently and it occurred to me that the story is supposed to be set in 2018. Given that that is only 4 years away and the fact that both Amy and Clara's world look remarkably like ours, we can conclude that Salamander and everything associated with that story were wiped from existence. In fact Amy and Rory should have gotten closest to 2018 given that in the Power of Three it was explicity stated that they sat at home for several years.
It does beg the question of how much of those older adventures can we still consider a valid part of the timeline. Indeed, its not entirely clear that a good chunk of the series since the restart in 2005 is still valid.
I tend to assume that any events involving a different world geopolitical situation pre-2006 from that which existed in real life was erased by the Time War. As far as I'm concerned, even if events happened to the Doctor and his companions, they've been erased from history; Whoniverse History, in my interpretation, matches real history until March 2006, when the Slitheen destroy Big Ben and assassinate Tony Blair in their bid to provoke a nuclear war.
One of the interesting things about RTD's tenure was that there was a larger meta-arc playing out in the background about how society comes to terms with the idea of alien life being real (and constantly attacking us). First they try denial ("Aliens of London"/"World War Three"), but as things escalate ("The Christmas Invasion," "Army of Ghosts"/"Doomsday"), a public debate emerges over whether or not to accept the seemingly unacceptable, and Harold Saxon takes advantage of this debate to promote himself on his way to becoming Prime Minister ("Smith and Jones"). The public debate is seemingly hijacked by Saxon before being settled when Saxon announces first contact with the Toclafane -- who then join with him to assassinate the President-elect of the United States in November 2008 ("The Sound of Drums"). (One presumes that only the subsequent assassination of Saxon by his own wife ["Last of the Time Lords"] and the discovery of Saxon's assassination of the entire British Cabinet at 10 Downing Street beforehand ["The Sound of Drums"] staves off a U.S.-U.K. war.)
By late 2008/early 2009, the public seems to have become inured to the repeated alien crises ("Voyage of the Damned," "Partners in Crimes"), and the world governments have developed contingency plans for united action in the face of a conventional alien military threat ("The Sontaran Stratagem"/"The Poisoned Sky"). The 2009 Dalek invasion removes the last visages of doubt (along, no doubt, with a significant portion of the world's military capability and economy), to the point where, in late 2009, as the 4-5-6 Crisis emerges, the new Prime Minister laments that the public expects him to protect them from threats no earthly power could possibly contain (
Torchwood: Children of Earth).
It's a bit of a shame that Moffat has more or less discontinued this exploration of how a post-First Contact Earth has evolved. Though the one time he
did spend a significant amount of time on present-day Earth in an alien crisis ("The Power of Three") suggests that world-wide alien crises have become an understood part of life, and that the public has more or less accepted that aliens are real.
Aliens have made public appearances and been on the news several times in the relative present since the show began. Yet each time, their arrival is treated as a shock.
I mean, even a public that accepts aliens as real is going to be shocked when they arrive and start a crisis. Knowing something in the abstract is not the same as expecting it on your doorstep.
Especially the kinds of aliens who tend to make their presence known to the public -- aliens who are
attacking human society. You may well know that terrorists exists in the real world, but that wouldn't make it any less shocking if they blew up your place of work or attacked the streets of your particular city.
things make even less sense when you factor in Torchwood. Miracle Day seemed to suggest that NONE of the alien encounters actually happened...or at the very least the CIA was unaware of them (which is impossible given that they were on the news).
I have no idea how to reconcile
Torchwood: Miracle Day with the rest of the Whoniverse, especially since its depiction of the months-long Miracle seems to in no way match Series Six's depiction of Earth in 2011. The only thing I can think of is that maybe
Miracle Day takes place in a timeline that branches off from the regular Whoniverse, and that it will eventually merge back into the main timeline at some point.
