Season 6B

Season 6B or Season 6 (b) is a revision and expansion to televised Doctor Who canon which places new adventures for the Second Doctor between The War Games and the first appearance of the Third Doctor at the start of Spearhead from Space.

The theory
To account to continuity discrepancies, Paul Cornell proposed the theory in The Discontinuity Guide which he wrote with Martin Day and Keith Topping.

The theory could explain the following continuity problems:

According to the Season 6B theory, 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 branch of the Time Lords. During this time, the Second Doctor apparently regains Jamie and Victoria Waterfield as companions, acquires a Stattenheim remote control device to summon his TARDIS, and undertakes an unknown number of missions, including that depicted in The Two Doctors. Eventually, either the Time Lords tire of keeping the Doctor on a leash, or the Doctor rebels and attempts to escape once more. This results in the exile which begins in Spearhead from Space (and presumably Jamie and Victoria were returned to their original times).
 * How the Third Doctor had several items not possessed by him before his trial (DW: Spearhead from Space).
 * How the Second Doctor, in DW: The Five Doctors, was aware that the Time Lords had erased the memories of Jamie McCrimmon and Zoe Heriot when he met apparations of the two in the Death Zone - even though the erasure took place immediately before the Doctor's apparent regeneration. (DW: The Five Doctors) (This is not a continuity problem. In "The War Games", the Doctor was told, point-blank that Jamie and Zoe would remember their respective first adventures with him and nothing more. What's more, immediately before his sentencing, the Doctor saw Jamie and Zoe back in their own times on a viewer and was told that they'd live out their lives as if nothing had happened. "Yes, very efficient," the Doctor said after seeing Jamie and Zoe back in their respective own times.)
 * Why the Second Doctor and Jamie appear noticeably older in their appearance in DW: The Two Doctors (especially the Second Doctor, who sports grey hair in the story).
 * Why Jamie McCrimmon can know about the Time Lords in DW: The Two Doctors.
 * How the Second Doctor could be working, apparently willingly, for the Time Lords in both DW: The Three Doctors and DW: The Two Doctors.
 * How the Second Doctor could possess a TARDIS recall device of a type the Sixth Doctor does not possess (DW: The Two Doctors).
 * How the Second Doctor's TARDIS has a different design in DW: The Two Doctors.
 * How the Second Doctor mentions that he is "a bit of an exile" in The Two Doctors, meaning that he WAS on exile and hadn't regenerated, and it WAS after The War Games.

To explain why the Sixth Doctor does not remember his own past in The Two Doctors, it is also suggested that the Time Lords wiped the Second Doctor's memory of the events of Season 6B (the Third Doctor did claim significant memory loss in Spearhead from Space). Alternate explanations have been made possible with the series revival, as the episode DW: School Reunion strongly implies that the Doctor retained no memory of the events of The Five Doctors, and the two-Doctor story DW: Time Crash implies the Doctor's memory of having met an earlier incarnation is triggered by the ringing of the cloister bell. Both of these can be used in support of suggesting the Doctor's memory of meeting himself in The Two Doctors was suppressed.

The feasibility of Season 6B is helped by the fact that at the end of The War Games, the Doctor is not actually shown physically changing appearance, unlike most other regenerations save the Eighth Doctor to the Ninth. Nor is any change depicted at the start of Spearhead from Space. (Note: it can by extension be speculated that the Doctor's aged appearance in The Two Doctors may also be the result of an interrupted regeneration.)

The Three Doctors
The Second Doctor is called on by the Time Lords to help the Third Doctor. But the fact that gives this away is that the Doctor is alone so it could be placed before The War Games but if this is so then when the Third Doctor makes contact with the Second, then the Second should know about his trial, his exile and regeneration(otherwise, this would prove that Time Lords have the power to send messages very carefully and not mention any events if the above is true). If this takes place after it, then this contradicts the aftermath of The War Games, as he is seen regenerating but otherwise, these events could have been prevented by the CIA.

The Five Doctors
As noted above, the Second Doctor claims that Jamie McCrimmon and Zoe Heriot should not recognise the Brigadier, as they had their memories wiped. (Although they were just illusions, so Rassilon might have done it as a trap.) Some evidence in dialogue confirm that this story happens after The Three Doctors. Since the Second Doctor would not be aware of the memory wipe if he was taken before The War Games, there is no easy way that he can know this, and still be the Second Doctor.1

The Two Doctors
The Two Doctors shows an aged Second Doctor traveling with Jamie on a mission for the Time Lords. The Time Lords have also built a device into the TARDIS console that gives them dual control. The Second Doctor states that working for them is the price he pays for his freedom. However, Jamie was not aware of the Time Lords until The War Games and a major plot point in that story is that the Second Doctor is and has for all previous stories been on the run from the Time Lords (This was confirmed as an error by the The Two Doctor's writer, Robert Holmes.) The aged appearance of the two actors also suggests it is after The War Games. The later Time Crash, however, attempted to rationalize the age differential issue but in fact does not as we see the Second Doctor and Jamie prior to meeting the Sixth Doctor and they are still aged.

The Doctor refers to Victoria as being part of the TARDIS crew, indicating the Doctor has been allowed to have her as a companion again. In World Game, however it is stated that this is a false memory given to Jamie by the Time Lords to explain her absense.

Novels

 * Players (a Sixth Doctor novel featuring a flashback to the Season 6B period]
 * World Game (set just before the Second Doctor's part of The Two Doctors from the point of view of the Second Doctor)

Short stories

 * Mother's Little Helper
 * Scientific Adviser
 * Reunion

Audiobook

 * Helicon Prime (with Jamie)

Other information

 * The idea of a post-The War Games Second Doctor, as Cornell acknowledges, had already been introduced in TV Comic. In Action in Exile, the Doctor arrives in London without his TARDIS and checks into the luxurious Carlton Grange Hotel. From this base, he proceeds to have five Earth-bound adventures, culminating in The Night Walkers, in which the Doctor investigates tales of walking scarecrows. He discovers that the scarecrows have been animated by the Time Lords to capture him, as the Doctor had escaped from the Time Lords before they could complete his sentence of a forced change of appearance. The scarecrows take him into the TARDIS and proceed to trigger his regeneration, leading directly into Spearhead from Space. (The scarecrows get a brief mention in the Doctor Who Unbound audio play Exile, and a variation is featured in the televised episodes Human Nature and The Family of Blood, which were written by Cornell.)
 * Aside from Jamie and Victoria, one other companion is known to have worked with the Doctor during Season 6B, a female Time Lord named Serena, who appears in PDA: World Game.
 * The early Doctor Who comic strips featuring the Second Doctor had him reuniting with John and Gillian, his grandchildren from the First Doctor comic strips, and sharing several adventures with them. As it's hard to rationalize where in the Second Doctor's TV timeline such travels might have occurred (given Jamie was with him for almost his entire life), it's possible these adventures also took place during Season 6B, although none of the stories make any reference to the CIA (suggesting they may have been part of the "on the run" storyline in TV Comic).