The Wormhole wrote:
Problem with that is, that the Doctor wouldn't be in good graces at all with the Time Lords right now, considering he destroyed/time locked them twice
Well, the Time Lords are opportunistic bastards who aren't above anything that has the end result of accomplishing their goals. All one has to do is think up a convoluted reason for how granting the Doctor a new set of regenerations is in the Time Lords' best interests and that takes care of that.
Or there's been a rebellion and that crazy ******* Rassilon and his cronies have been removed. But rather than making the Doctor their darling, they're now led by a somewhat reformed Master. So, our hero is allowed to continue doing what he does and is sometimes even supported from a distance, but is kind of persona non grata
on Gallifrey. Just like old times.