30. Why Were The 2nd Doctor And Jamie Working For The Time Lords In "The Two Doctors?"
Previously it was understood that the 2nd Doctor, like his predecessor, was on the run from his own people. So how did he come to be calmly acting on their behalf in "The Two Doctors?" Also, companion Jamie McCrimmon had never heard of the Time Lords before the 2nd Doctor' swan song serial The War Games, so how could he be aware of them before then? Paul Cornell, Martin Day and Keith Topping in The Discontinuity Guide came up with a theory that many Whovians have embraced.
"Rather than undergoing the regeneration shown starting at the end of The War Games, the Second Doctor was recruited to work for the Celestial Intervention Agency, a clandestine Time Lord organization shown to exist in TV: The Deadly Assassin. "During this time, the Second Doctor regained Jamie and Victoria as companions, acquired a Stattenheim remote control device to summon his TARDIS and undertook an unknown number of missions, including that depicted in The Two Doctors. "Eventually, the Doctor's association with the CIA ended for reasons not known and his full War Games sentence was executed at the beginning of Spearhead from Space."
This explanation was never given on screen and certainly makes sense but is it the answer?