In the closing episodes of ‘the War Games’ the Doctor realises he will need the help of his own people, the Time Lords, to fix the damage done by the War Lord and War Chief.

Knowing that he will be punished by the Time Lords he tries several escape attempts but they outsmart him at every turn and put him on trial. 

His companions, Jamie and Zoe would be sent back to their own times, remembering only their first encounter with the funny little Time Lord.

Despite the Time Lords acceptance that he was doing right in his adventures, and fighting the evil that dwells in the universe they would still punish him for his transgressions, sending him into exile, and changing his appearance for the second time.