On a world with no name, (maybe it shall have one, probably not), two commercial time travellers (they deliver product a millisecond before your order is processed), who shall be known as Owen and Bill (because every active time traveller takes a false name or a title, makes it harder for folks to kill you when you were young or do similar tricks) are blacklisted from their world's Society Of Time Travellers for one and a half millennia. Now being blacklisted is a punishment that stretches down to the genes, no time vessel of their kind's make will let them pilot unless accompanied by unblacklisted members who are on board of their own free will.
Note the story takes place in a different fictional universe than Who so no need to take "canon" into consideration.
After a few years fuming the two decide "screw this" and steal two newborns (although they look and act five or six, imagine if Lungbarrow style looms created much younger looking product, also they shall be called the Boy and the Girl, or Clara and Dylan) future members of the Society, using them to gain access to a Time-ship (who's rather annoyed by the whole thing) and head of into space-time.
They are pursed by the Warden and the Statician (who's pissed that they've messed with the census), our other protagonists.
The story spans two thousand subjective years and is an exploration of how wandering adventureres would likely affect a wide universe, whether the Doctor's philosophy of "go against society and be awesome" is really worth pursuing, or maybe he (and by extension Bill and Owen) should have been captured by their respective societies.
Basically anyone who's ever had a niggling thought about the Doctor Who franchise, explain it at will.