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Regeneration is the process by which the Doctor and other Time Lords maintain their centuries-long lifespans. It is generally concieved of as a "genetic reshuffling" which a Time Lord may go through if his body is worn out by age or has suffered some life-threatening injury or infection. Time Lords may even regenerate at will.
Control over Regeneration
While the Doctor apparently has never had much choice in what the finished product looks like, others, like Romana, seem adept enough at the process to custom design their new appearances, as demonstrated in the opening scene of "Destiny of the Daleks," when she went through several bodies before finally deciding on a copy of Princess Astra. This is most likely because all the Doctor's regenerations have to date been involuntary, the result of mortal injuries or, in one case, having a regeneration forced upon him by the Time Lords prior to his exile on Earth at the end of "The War Games."
Development of the Concept
Regeneration was first introduced when the First Doctor (William Hartnell) changed into the Second Doctor (Patrick Troughton) in the closing moments of "The Tenth Planet." Tradition has it that Hartnell himself thought up the idea of the Doctor being able to change into a new body as a means of keeping the series going after his departure. In "Power of the Daleks" (the first story featuring the Second Doctor), the Doctor described himself as having been "renewed", and also said that the change was "part of the TARDIS."
The process was not actually referred to as "regeneration" until the end of "Planet of the Spiders," when the Third Doctor (Jon Pertwee) changed into the Fourth (Tom Baker). Prior to this, the Doctor was simply described as having "changed his appearance."
Limitations
It was established in "The Deadly Assassin" that a Time Lord can regenerate twelve times before permanently dying, though as with most such "rules" there were occasionally exceptions. For more on this see the Time Lord article.
In "The Brain of Morbius" (produced shortly before Assassin), it was implied through visual images displayed during a mental battle between the Doctor and Morbius that the Doctor had at least eight incarnations prior to the First Doctor. However, multiple dialogue references throughout the series (particularly in The Three Doctors and The Five Doctors) contradict this, as well as the fact that the Doctor has regenerated three times since Peter Davison's tenure. Explanations by fans have included theories that the images were of Morbius's previous incarnations or that they were false images induced by the Doctor. Yet another possibility, suggested by the Virgin New Adventure novel, "Lungbarrow," is that these were the Doctor's incarnations during his previous existence on Gallifrey as "the Other."
In some circumstances, a Time Lord may be unable to regenerate, despite having an ample number of lives still available. The Elixir of Life, distilled by the Sisterhood of Karn from their Sacred Flame, can help in these situations.
The Doctor's arch-enemy the Master found his own remedy for the end of his regenerative cycle. He first attempted and failed to use the Eye of Harmony on Gallifrey to renew himself, though he was able to absorb enough energy from it to extend his life for a time. He was finally able to gain access to the Source on Traken, and used some its powers to steal the body of Nyssa's father Tremas. When this body was finally destroyed by the Daleks on Skaro, the Master's essence entered that of a human on Earth, and in this body the renegade Time lord tried to use the powers of the Eye of Harmony's dimensional link on the Doctor's TARDIS to steal the Doctor's remaining lives.
Rassilon is said to have achieved a cycle of perpetual regeneration, becoming immortal. It was for this secret that Lord President Borusa sent four of the Doctor's incarnations and their companions into the Death Zone, where Rassilon lay in eternal sleep in the Dark Tower. It may also have been this particular method of perpetual regeneration which Mawdryn and his team of scientists attempted to steal from the Time Lords, with the result that they became undying creatures who continually aged and renegerated until the Doctor was able to finally help them die. Legends mentioned in the Virgin Missing Adventure novel "Goth Opera" suggest that Rassilon became immortal when he was turned into a vampire by the Great Vampire himself.