2. With The Time Lords
Of course, if the War Doctor chose a path towards goodness and offered his services to his people willingly during the Time War and beyond after all, just because Gallifrey is now frozen in its own pocket universe doesn't mean it can't be invaded or caught up in conflict later on that could make for a great story arc. Being the Doctor, though, he surely couldn't just play at being the good soldier and act on orders from above. He most likely wouldn't stand for it, and if he did it just wouldn't be the same. Far more entertaining would be clashes between himself and the higher-ups of the Gallifreyan army. Whether that's The General or a resurrected Rassilon as in 'The End Of Time', or even one of the Romanas (after all, she does serve as Lady President in her own audio series), it's a tough choice. What if indeed the War Doctor were chosen for this highest of responsibilities to his home planet? But whoever serves as President or commander in chief, and their battles of wits with the Doctor, would make for utterly compelling viewing. We've seen the Second Doctor rail against his own kind in The War Games, the Fourth revisit Gallifrey in The Deadly Assassin and 'The Invasion Of Time and the Fifth battle Omega in Arc Of Infinity, but this would surely take it all to an awesome conclusion. And what if he somehow got the chance to interact with Rassilon and Omega once more, as he's alleged to have done in the very founding of Gallifrey an event his Seventh incarnation seemed desperate to cover up? The idea that the War Doctor could have been one of the true founders, at least in the sense that he helped lead his people to become what they did and overthrow the Cult of Pythia to usher in the era of the Time Lords and ensure the triumph of cold hard science over ritual is one that should have every hardcore Whovian salivating. After all 'The Other' could have been the first in a string of this Doctor's forgotten aliases cooked up in a bid to preserve his mystique...