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In the Doctor's first trial involving the Time Lords, he was charged with breaching the non-interference policy and tried by a court of Time Lords. (TV: The War Games) The trial was dubbed in the official court records as "Malfeasance Tribunal 309906". (TV: The Deadly Assassin, PROSE: A Brief History of Time Lords)
History
Origins
Prior to the trial, the Doctor had been hiding from the Time Lords due to violating their laws. By one account, he was put on trial solely for the charge of breaking the non-interference policy. (TV: The War Games) Other accounts indicated he had two charges, but that the second, stealing a TARDIS, was incredibly minor compared to the first. (PROSE: The Trial of Doctor Who, Doctor Who and the War Games) A third account indicated his charge was breaking the First Law of Time by meeting the Sixth Doctor while on a mission from the Celestial Intervention Agency, and that he'd only been hiding from the Time Lords since then. (PROSE: The Legacy of Gallifrey)
Judging the return of the participants in the War Games too tough a task, the Second Doctor decided to send a hypercube containing all the relevant information to the Time Lords so that they could help with the matter, although the War Chief quite forcibly advised against it. (TV: The War Games) In the timeline as it stood after Rassilon used an amnesiac Eighth Doctor to make "one or two small improvements in the patterns of history", the Second Doctor was aided in this decision by the Eighth Doctor, who suggested a defence speech to his past self which the Second Doctor would recite nearly word-for-word in the trial. (PROSE: The Eight Doctors, World Game) Authorities from Gallifrey were dispatched to the planet, including no lesser Time Lords than the Keeper (PROSE: Doctor Who and the Doomsday Weapon) and three members of the High Council, (PROSE: The Three Doctors, The Legacy of Gallifrey) one of them being Goth, (PROSE: The Legacy of Gallifrey) who was also an agent of the Celestial Intervention Agency, (PROSE: Future Imperfect) yet unknown to the Presidency. (PROSE: The Legacy of Gallifrey)
The Doctor briefly attempted to evade the Time Lords but they took control of the TARDIS and landed it on Gallifrey. The Doctor, Jamie and Zoe witnessed the War Lord being sentenced before Jamie and Zoe were placed in a force field and the Doctor was escorted to his own trial. (TV: The War Games)
The recorded trial
The court accused the Doctor of breaking their laws of non-interference. The Doctor admitted the crime and reiterated his pride in doing so, rather than merely observing the evil in the universe. He then asked for a Thought Channel to show the evil he fought. He showed the Time Lords the Quarks and the Yeti. When they seemed unimpressed he showed them the Ice Warriors, the Cybermen and the Daleks. He ended by saying that he may be guilty of interference, but they were guilty of passivity against such evil. With the trial over, the Time Lords considered the charges whilst the Doctor played cards.
Allowed to bid farewell to Jamie and Zoe they convince him to try and escape but they are intercepted by a group of Time Lords. The Doctor says goodbye to both of them before they are returned to their own times with their memories wiped of all but their first encounter with the Doctor. The Doctor watched on a screen as Zoe is returned to the Wheel and Jamie fights a Redcoat.
The Time Lords then delivered their verdict; they accepted that there was evil in the universe that must be fought and the Doctor had a part to play. 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. He then lost his speech and began to swirl into nothingness. (TV: The War Games)
The trial's secret facets
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Before the Doctor's sentence could be carried out, the Celestial Intervention Agency intervened and turned him into their "hired gun". (PROSE: World Game) He worked in this capacity for some time, (TV: The Two Doctors et al.) although he was unaware of the true extent of this. Knowing the Doctor was liable to becoming impatient and feeling exploited, the Time Lords took to wiping his memory after each mission. The result was that the Doctor believed every mission to be his first and readily accepted them, led as he was to believe each time that success would grant him his release. (PROSE: Save Yourself) However, when the CIA needed to cover up his visit to Space Station Camera, it was decided that his exile should be enforced. (PROSE: A Brief History of Time Lords) Before he could be forced to regenerate, the Doctor finally succeeded in escaping. He settled down on Earth in hiding, though lived there in luxury for some time, before falling into a trap and finally regenerating into his third incarnation. (COMIC: The Night Walkers)
Legacy
Because the Time Lords knew little about the human mind, both Jamie (COMIC: The World Shapers) and Zoe were able to regain some of their memories of travelling with the Doctor. (AUDIO: Echoes of Grey) Additionally, after the Doctor had saved the Time Lords from certain doom they lifted his exile and restored his knowledge of the TARDIS. (TV: The Three Doctors) On the day of Pandad IV's assassination, Spandrell and Engin consulted the Doctor's entry in the APC Net, learning of this trial. (TV: The Deadly Assassin) This trial was referenced during the Sixth Doctor's trial for meddling, in which the sentence was deemed by the prosecutor to be too lenient. (TV: The Mysterious Planet)
It was during the trial that the Doctor first directed the Time Lords' attention towards the Daleks. (TV: The War Games) The Time Lords monitored the Daleks' continued activities and partially came around to the Doctor's way of thinking, viewing them as a potentially serious threat. (AUDIO: The Dalek Conquests) Eventually, they summoned the Fourth Doctor to Skaro to avert the creation of the Daleks. (TV: Genesis of the Daleks) The failure of this mission eventually prompted the Daleks to retaliate, resulting in mounting aggression which led, in the longer term, to the Last Great Time War. (PROSE: A Brief History of Time Lords, The Slyther of Shoreditch, Engines of War, et al.)
Other realities
In a parallel universe, the Second Doctor chose one of the faces offered to him and became a brutal dictator on Earth. (PROSE: Timewyrm: Revelation)
Behind the scenes
The concept of a Season 6B set between The War Games and Spearhead from Space was a long held fan theory and established as narrative fact by TV Comic.
In the fan film, Devious, the Doctor was extracted by the CIA halfway through his regeneration creating the "Second-and-a-Halfth Doctor" played by Tony Garner. He went on several adventures before completing his regeneration.