Second Doctor's change of appearance

"Fear no more, Hogan... After this dreadful night has passed your scarecrows will not walk again!"

- The Second Doctor's last words

Following the Doctor's trial, the Second Doctor was sentenced by the Time Lords to undergo a "change of appearance" into the Third Doctor, (TV: The War Games, COMIC: The Night Walkers, PROSE: Doctor Who and the Auton Invasion, etc.) a process which later sources referred to as a regeneration, (PROSE: Timewyrm: Apocalypse, World Game, AUDIO: The Final Beginning, etc.) the second of what the Eleventh Doctor understood to be his original life cycle. (TV: The Time of the Doctor)

Nature
By early accounts, this event was termed a "change of appearance". (TV: The War Games, COMIC: The Night Walkers, PROSE: Doctor Who and the Auton Invasion, Lourdwater Cottage Hospital case summary, The Three Doctors, Doctor Who and the Giant Robot)

Later sources clarified this event as a regeneration. (PROSE: Timewyrm: Apocalypse, World Game, AUDIO: The Final Beginning, etc.)

Sentencing & choice of appearance
They noted his affinity to Earth and told him he would be exiled there as well as forced to regenerate. The Time Lords gave the Doctor several choices for his new body but he declined all of them. (TV: The War Games)

At the courtroom
In the public account of the trial, (PROSE: World Game) the Second Doctor, after rejecting the choice of faces offered to him, then lost control of his speech and facial muscles, finding himself babbling and involuntarily gurning. As he fought to regain control of his body, resisting the process, the Doctor found himself in a dark void, orbited by swirling images of his own face. His head then abruptly vanished, leaving him clutching with both hands at the empty space where his face had been, but still able to speak. He exclaimed that he felt "giddy", and told the Time Lords theu, "[could]n't do this to [him]" Finally, the headless Doctor was sent twirling into nothingness. (TV: The War Games) This was, by some accounts, the Doctor's regeneration, (PROSE: Lungbarrow) a typical example of the Disciplinary. (PROSE: How to be a Time Lord)

By one account, the Doctor's life passed before his eyes as he regenerated, thinking of all his past companions from his incarnational lifetime. Just before the Doctor's regeneration ended, his "mind was opened, and his entire past and future shone, cruel and clear, before him" and, realising what he had done on the Panjistri homeworld, he sent a telepathic warning to the Seventh Doctor about the Timewyrm. (PROSE: Timewyrm: Apocalypse)

On Earth
By one sequence of accounts, the Second Doctor was exiled to Earth (COMIC: Action in Exile, etc.) but managed to escape the Time Lords before they could carry out the second half of their sentence. He managed to live for some time on Earth, but was eventually attracted to a mystery involving animated scarecrows

The scarecrows dragged him to his waiting TARDIS, where they forced him to regenerate. During the process, the scarecrows programmed the TARDIS for a final flight. (COMIC: The Night Walkers)

Recovery
During the change of appearance, the Time Lords had edited the Doctor's memory to remove his knowledge of how to work his TARDIS, (TV: Spearhead from Space, The Claws of Axos) restrict what he knew about other alien species (PROSE: The Ambassadors of Death) and events beyond the 1970s. (PROSE: The Devil Goblins from Neptune)

The TARDIS travelled to an English field, where it was found, along with the newly regenerated Doctor, by UNIT. (TV: Spearhead from Space)

Legacy
Later Doctors would remember being executed at the trial. (PROSE: The Eight Doctors; AUDIO: Legend of the Cybermen, Stage Fright)

Seeking to enlist the Second Doctor to assist the Third Doctor in the First Omega Crisis, the Lord President instructed a Junior Time Lord to access the section of the Doctor's time stream "for his earlier self before he changed his appearance". Upon coming face to face with the Second Doctor again, the Brigadier initially believed that the Third Doctor had changed back to his earlier appearance before learning that this Doctor was from the past. (TV: The Three Doctors)

When the Third Doctor disappeared prior to his regeneration, the Brigadier told Sarah Jane Smith that the Doctor had previously been away "for months" before turning up with a new face, "could have been a completely different man". (TV: Planet of the Spiders)

Much later from the Brigadier's perspective, he had a reunion with the Second Doctor, who noted that he was "bending" the Laws of Time by being there. At this point, the Second Doctor remembered both the confrontation with Omega and his own replacement, who he commented was "pretty unpromising". (TV: The Five Doctors)

The Spy Master, whilst preparing to subject the Thirteenth Doctor to a forced regeneration, noted that it was the ultimate sanction for breaking the Time Lords' laws and recalled that they had punished the Doctor accordingly once before. He went on to suggest that they had done this more than once, and that the Doctor would have not have known. (TV: The Power of the Doctor)

Other realities
In a parallel universe, the Second Doctor had regenerated into one of the faces offered to him by the Time Lords. This new incarnation became known as the Leader, the President of the Republic of Great Britain. (PROSE: Timewyrm: Revelation, TV: The War Games) Another account indicated that the Leader was not the Doctor but rather a human, and was ultimately killed on Earth. (PROSE: I, Alastair)

In the Unbound Universe, the Second Doctor regenerated into a third incarnation who arrived on Earth in Hong Kong on 30 June 1997. (AUDIO: Sympathy for the Devil)

In another universe, the Doctor escaped the Time Lords and committed suicide, regenerating into a female incarnation in an attempt to elude them. (AUDIO: Exile)

Behind the scenes

 * The fan serial Devious, part of which was featured on the DVD release of The War Games, featured Tony Garner as "Second-and-a-Half Doctor", an amalgam of the Second and Third Doctors created when the regeneration of the former into the latter was stopped halfway. This Second-and-a-Half Doctor came face to face with the Third Doctor, with Jon Pertwee reprising his role, before completing his transformation into him, leading directly to Spearhead from Space using footage from that story. The commentary of Devious acknowledged that Pertwee appeared visibly older than he did in Spearhead from Space whilst deriving an explanation from the television story The Christmas Invasion, a comparison being drawn between the Tenth Doctor's replacing his lost hand and the Third Doctor growing "younger."