And there's nothing like a Time Lord regenerating into a new actor to get you thinking about a reappearance by a former self.
This is easier if different incarnations were played by different players anyway, so you don't have one player stuck with multiple versions of their Time Lord PC, but this is best done if the Time Lord changed players between regenerations anyway. Having one player imitate another player's character rarely works well.
Even if the Time Lord stays in the hands of the same player there are still a few tricks to use, like splitting the party with different incarnations going with different groups, or having the incarnations phase in and out but there's only one on-screen at a time. (Er, yes, that is the trick from Dimensions In Time. Shut up.) The presence of multiple versions of one character in a game about time travel leads pretty directly to ideas to do with wibbly-wobbly timey-wimey issues, so use them to your advantage. If in doubt, you can always blame ancient Time Lords threatening to return from beyond death.
You could do something as big as The Ten Doctors but probably best not to try it in a single session.
Of course, if you really want to mess with the format, consider making the promise of The Next Doctor true, and bringing in a future incarnation. It helps here if you have a plan in mind for a possible regeneration and its effects, but it isn't essential. Just take a guess based on any previous regenerations, perhaps talking the idea over with the Time Lord's player. You could make the new version radically different as foreshadowing of events in the current incarnation's personal future, and the future self could drop hints of what caused the change, while naturally being guarded about the specifics to avoid a massive paradox. And if this future self doesn't happen, it could always be an incarnation from after the series, or a parallel timeline, or a halfway regeneration or... something.
I have an idea for a convention one-shot where everyone gets to play an aspect of the Doctor that never existed, after the current Doctor gets blasted by a phlebotnum effect that splits him into half a dozen possible versions based on elements of his personality. (With most fictional characters, splitting into good and evil would be done with split screens and the same actor, but with the Doctor it could be an excuse to recast multiple times.)
And the Companions are still there, trying to deal with this. And whatever caused this, it's obviously big enough to threaten time and space as well as being an excuse for a nostalgiafest.
And if there was ever an excuse to bring back a villain particularly associated with a former regeneration, this is it.