I just read this on IMDB, have no clue if it's accurate, just re-posting whats been claimed there.
"This is not a drill, spoilers ahead.
Since syphoning off his regeneration, the next Doctor that was being 'born' remains inside much like the Master's identity within Yana in Utopia. The new Doctor begins to manifest after the Doctor is wounded, resulting in a somewhat schizophrenic change over that lasts almost all the second part of The End Of Time and a final regeneration "like a steam pipe with enough pressure to rewrite the DNA of everything for fifty yards". This causes a mad dash for a 'death' alone in The Tardis. The outfit is wrecked, so is the interior of the Tardis, resulting in a redesign. David and Matt share screentime with some spooky sfx throughout the episode. Four times. The knocking is not literal and is not The Master, that was a deliberate metaphor which combined with the presence of the Master is known to serve a big red herring. The new Doctor knocks four times.
The something coming back through the dark is also the same reason why Dalek's are in the next season despite the genocide in Journey's End; the planet Gallifrey is coming back into existance as time rewrites itself now that the time lock has been broken on The Time War by Dalek Caan, and further interferance has taken place. This saves the Dalek's and The Time Lords, and creates a 'cold war' of time that will see other races brought in on both sides. The new Doctor is considered a fugitive, as the killer of his own kind. In many ways the next season resembles Firefly, in the space wide rebellion/politics way of things."
and further in the thread...
"I've also been told some stuff about Dalek's trying to turn humans against Time Lords by giving the humans technology long ahead of time, in a bid to make them advance technologically far out of synch with any humility of their place in the universe. Which sounds interesting to me, and I have heard a recording where a scientist is explaining to the Doctor that he is recieving these inventions in his head randomly, without working on such designs.
The details I have to me are far too meticulate, and fit far too well, for me to dismiss outright as a hoax, ergo I post the details for debate (more so than to debate the validity of the claim - let's face it, I'm never going to name my drinking buddy)."
"Apparently The Tardis is totalled because it is a living organism. It has often been referred/inferred to as alive (reference; Boom Town, Turn Left), ergo it is prone to damage by such a blast, where as inanimate clothing is not. The outfit is damaged by the destruction of The Tardis more so than by the energy itself. Given the energy is Time Lord stuff, and so is The Tardis, it makes sense it could overload and go to pieces.
I think with the time line being rewritten, everytime it happens things afterward change, but the 'time' that happened before the change remains constant for the change to have taken place, even if it only remains constant for the people in 'the eye of the storm' (reference; The Last Of The Time Lords) or perhaps encased in a Tardis, or in its viscinity, as The Tardis does generate a kind of energy/cloak that can be residual (reference; pilot of Torchwood).
I've also been told there will be one episode specifically about growing a Tardis, which in addition to being pretty cool (and no doubt called something like The Garden Of The Tardis) would be a perfect opportunity to explain any Deus Ex Machina about time lines. After all, it is Time And Relative Dimension In Space.
To be honest, I liked the idea of the Doctor being the last of his kind, but with The Master coming back again its obvious this is no longer a priority core design for the show, and frankly on the subject of Deus Ex Machina...if he's going to beat the maximum regeneration total allowed (and ratings will no doubt dictate he will) it makes sense that Gallifrey will have to be around, just like Davros had to come back last time to explain a new era of Dalek. I doubt the Doctor will find The Orb Of Extra Regeneration on some far flung planet and get away with it against the audience."