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Quoth Racket_Man
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There is some evil in all of us, Doctor, even you. The Valeyard is an amalgamation of the darker sides of your nature, somewhere between your twelfth, and final incarnation.
As to the exact mechanics of regeneration, we're not exactly sure. Each one has been different, to whit:
1) The Doctor's body succumbs to old age during the battle with Mondas and the Cybermen, he collapses inside the TARDIS and regenerates.
2) The Time Lords (in their first mention and on-screen appearance) put the Doctor on trial for his continual intervention in the affairs of lesser races, and sentence him to exile on Earth in the 20th century, locking away his knowledge of dematerialization theory and breaking the dematerialization circuit in his TARDIS, forcing him to undergo a regeneration as part of his sentence (though there's evidence that they had him perform a few 'unseemly' tasks for him first, "The Two Doctors" can't have taken place at any point in the second Doctor's timeline except after his trial, but he was supposedly forced to regenerate and shipped to Earth instantly after the trial).
3) The Doctor suffers from a massive dose of radiation from a 'web' made of Metabilis 3's Blue Crystals when he confronts the leader of the giant spiders that rule the planet. He stumbles back to the TARDIS, and spends (according to the supplemental materials of the series) nearly a century wandering, sick with radiation poisoning, through time and space, before finally returning to Earth, collapsing in front of the Brigadier and Sarah Jane and finally regenerating.
4) The Doctor falls from the scaffolding of a radio telescope.
5) The Doctor and his companion Peri are poisoned after contact with a spectrox web and are slowly dying of Spectrox Toxemia. The Doctor travels deep beneath the surface to obtain the milk of a queen giant bat, the only known cure, but accidentally spills some. He gives what's left to Peri to cure her, then succumbs to the poison himself and regenerates.
6) The exact circumstances are unknown. The Rani hijacks his TARDIS somehow, forcing it to land on the planet Lakersia, where she is conducting her latest cruel experiment. Supplemental materials have the Doctor explain that he willingly gave up his sixth incarnation because it had run it's course of usefulness, and he knew that he would need to become the Hero of Time, a feat that his sixth form would never have been able to handle.
7) The Doctor is shot by a gang on Earth after the Master's remains force an emergency landing there.
8) Unrevealed as yet.
9) Absorbing the Time Vortex's power from Rose's body into his own.
10) Saving Wilf's life by taking the radiation blast from the machinery himself. As with his third regeneration, the radiation poisoning is slow, and he makes it a point to travel to see his former companions, giving them one last moment with him before returning to the TARDIS to allow the regeneration to proceed.
As to the end of the Time War:
Gallifrey is gone. The Doctor either blew the entire planet up, or scorched it with whatever weapon he used to destroy the Time Lords and the Dalek fleet. Make no mistake, the Time Lords are gone. They are not "alive" in any true sense of the word. They 'exist' inside the Time Lock that engulfs the War, but Time Locks act like a door: nothing inside the Lock can pass beyond a given moment in time. In this case, the Lock's defining termination point is likely just after Gallifrey is scorched by the Doctor. The events of "The End of Time" were the Time Lords attempting to escape the Lock by using the Master and the Doctor, and extracting Gallifrey from the Lock to overlay and replace Earth with it. However, such a massive strain on reality would have shattered the Time Lock, allowing all the horrors of the Time War to spill out everywhere and everywhen again, with no way to stop it. The Master shattered the diamond that the Time Lords were using as a physical 'bridge' to pull Gallifrey out of the Lock, and then allowed himself to be drawn back into the Lock, so that Rassilon could not attempt to use him the same way again.
Best way to think of the Time Lock, though, is this: The Lock is like a gigantic stone wall that was constructed around the war. No matter what era any given battle of the War took place in, no one and nothing (save accidents, like Dalek Caan) can every penetrate the Lock and observe or affect the events. Simply put, the War itself got "shifted" like the Medusa Cascade, just enough so that it's out-of-sync with Time itself, and thus impossible for anyone to enter or exit.
But I loved it anyway!
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