Ian and Barbara left the show almost at the end of the second season, firmly cementing the idea that, in Doctor Who, all companions are temporary. Indeed, the Doctor goes on to have a further six companions over the course of the next twelve stories. I'm going to deal with two of those quite briefly, because they're difficult to fit into a game that sticks to continuity, and I'm going to pass on Ben and Polly altogether for now, because I feel they more properly belong with the second Doctor.
And I'm going to ignore John and Gillian on the grounds that who the heck wouldn't?
That leaves me with two that deserve more discussion. In our imaginary TV-show-as-RPG-campaign, Barbara's player has decided to leave the group. The GM incorporates a method for her character and Ian to finally get back to their own time into his latest scenario, thus completing their plot arc. Ian's player agrees, because it fits the story, and the two metaphorically walk off hand in hand into the sunset.