I haven’t heard how the whole “cracks in the universe” thread was resolved, but here’s my not-so-serious take on how it ought to have gone.
The TARDIS materializes in a gray void. Its scanners say that there’s a livable environment outside; the Doctor makes references to "The Mind Robber" and "Warrior’s Gate". The Doctor, Amy, and Rory step out, and come upon a table, at which are seated both the White Guardian and the Black Guardian*.
The Doctor brings up the Key To Time. The White Guardian says that it wasn’t so much the actual Key that he needed, but it was the act of collecting the pieces that set in motion the events he wanted done. The Black Guardian comments that destroying the Key and sending the pieces back helped him maintain the balance between the two Guardians.
The White Guardian cuts short the chit-chat. There’s something afoot that, if not stopped, could utterly destroy the entire universe. And for real, this time. He may have already noted the cracks...
It seems that the Time War was supposed to effectively remove BOTH the Daleks and Gallifrey/the Time Lords from the universe, but the Daleks haven’t gone away. The White Guardian displays a picture of a man who looks remarkably like Russell T. Davies, and says that he is the focal point of the situation.The Doctor must decide to either totally erase the Daleks from existence, or bring back the Time Lords. If he does nothing, the continuity stresses will result in the absolute, irrevocable End Of Everything. For Real. He has to go back in time, find that man, and convince him to stop messing with the continuity of the universe.
* I know there’s no chance of getting the original actors, but they are superpowerful beings who can appear in any form they like.
Yes, I thought the Daleks were supposed to have been wiped out. Twice, by my count. Why the hell do they keep coming back, and the Time Lords are reduced to a spittle-spewing Timothy Dalton in a special episode?