Disclaimer: this is a work of fiction.
Part Three: Crisis
The root of the problem was that Saward wanted a darker feel to the series, and Baker wanted a darker Doctor to go with it - this would help contrast with his predecessor’s portrayal of the role (though Baker planned to soften him over the course of the years he intended to play the Doctor for). JNT initially supported this position, for the reason that it provoked outrage amongst Mary Whitehouse’s NVLA which, perversely, always resulted in a subsequent boost in ratings. But this darker feel had not been introduced in Twin Dilemma (for reasons outlined above), and so the split was between JNT, who came to believe that they needed to continue in the same vein as Twin Dilemma, and Saward and Baker, who wished to carry on with the intended change in emphasis.
Saward’s position seemed strongest at first - the script for Attack of the Cybermen (planned as the first serial of season 22) was already written, and he had edited it heavily to deliberately contrast it with Twin Dilemma (so the change in the character of the Doctor would not seem arbitrary). If it was to be changed, time was against them.
JNT then pulled a masterstroke. He invited Saward and Baker to a lunch meeting with himself and two old stalwarts of Doctor Who: former Producer Barry Letts and former Script Editor Terrance Dicks. At this (now legendary) lunch a compromise was reached - Letts and Dicks convinced first Baker and then Saward to abandon the ‘darker’ Doctor, and Dicks agreed to assist Saward in making the necessary changes to the scripts. In return, the darker direction of the stories themselves would be kept. To help with this, a second Companion would be introduced who would take on some of the role originally intended for the darker Doctor.