1. He escapes to France and finds the McLarens working for a rich couple in Nice. There he becomes a hostler, learns enough French to get on, and baby sits Kirsty’s sons, Benny and Alex, when she goes with her husband Louis to Paris one summer. The boys think of him as their uncle, but don’t really like the stories he tells because none of them seem to have good endings and the hero is faceless.
Once it is safe for them to return to Scotland, he does, although the others elect to stay behind with Laird Colin, who is ailing. In Scotland, he goes back to his hometown to find it a different place, but he’s used to having to pretend to be someone besides a Highlander by now.
He marries a nice woman, they have three kids (Ben, Robert, and Victoria), and he spends the rest of his life as a shepherd. Rob learns the bagpipes, Victoria marries an Englishman, and Ben goes into the Navy. He lives to a ripe old age and passes on ten years after his wife does. He’s buried next to her in a tiny, windblown cemetery.
2. The Redcoats send him to the Americas when they catch him, but instead of working off his sentence he runs away and ends up in Boston somehow, a few weeks later. Unfortunately it’s winter, so he collapses half-frozen in the street and has to spend the night in the jail, but at least it’s warm. He gets a job working as a janitor for a lawyer, whose daughter develops a crush on him and teaches him to read more than just his name. He devours every book he can lay his hands on.
Eventually he marries the lawyer’s daughter and starts apprenticing in a print shop, which he takes over from the original owner after a few years. He prints newspapers and things, and is happy to print brochures that rail against the crown. He also prints small books of stories that he writes for his daughter. He doesn’t try to sell them to papers, though. Who would want to read about a Scottish teenager traveling to other worlds?
3. It wasn’t the best idea, really, to charge a man with a gun when only in possession of swords. Brave, perhaps, but stupid. Naturally, he gets shot. The Time Lords think it’s best that the Doctor never find out.
4. You wouldn’t think it possible, but the Time Lords screw up and send Jamie and Zoe to the wrong places. She ends up inventing several pieces of important technology centuries too early and he just sort of wanders around until someone sends him off to a colony world where he’ll be happier. Obviously, this is a problem, so the Time Lords have to go fix everything. They bring Zoe back to her time, but leave Jamie alone because he’s not causing any problems. They live on the colony world together as a pair of decided old bachelors and bicker until the day they die.
5. Possibly the Time Lords only send Jamie to the wrong time. He appears out of thin air somewhere in Scotland in the 70s and runs into Sarah Jane, who has very recently been dumped in Aberdeen. Once she figures out that he’s from the past, she takes him home with her and presents him to UNIT. They figure out who he is and that he’s forgotten his adventures because the Brigadier remembers him, but Jamie doesn’t remember the Brigadier back.
Although thoroughly weirded out by the idea that he’s lost many of his most important memories, he starts working for UNIT. They hope that fighting aliens will trigger his memory, but it doesn’t ever work, unfortunately.
That’s alright, though. He makes new memories.
6. The first thing the Doctor does when he thinks he’s fixed his TARDIS is try to go back and find Jamie and fix what was done to him. He gets there fifty years too late and the next try takes him to Venus after its colonization. While exploring, he comes across an old memorial. He recognizes it as a memorial to all the useless deaths in war, made during a time in humanity’s history enlightened enough to realize the evils of fighting and misunderstanding. His former self would have probably scratched a few more names onto the stone, but as he is, he leaves it.
7. He is captured by the Redcoats and after he admits quite proudly to being a Jacobite, they hang him. It’s historically accurate, anyway.
8. The Time Lord’s hold on the Doctor’s TARDIS isn’t quite as strong as they might have liked and he is able to escape long enough to leave Jamie and Zoe in safe places. They protest, naturally, but he puts a few sleeping pills in their tea. He’ll be light years and millennia away before they wake up. They’ll do alright, he thinks, in 1960s Britain. He’s just not quite sure what Polly’s reaction to finding them on her doorstep in the morning will be.
9. I suppose it’s possible that the Time Lords just plain never caught up with the Doctor. But if they hadn’t, would Jamie and Zoe have ever left?
10. The CIA gets a hold of the Doctor before he can regenerate and gives him missions to run for those terribly hypocritical Time Lords. He asks for his companions back, naturally, memories intact. They only give him Jamie. It seems a little cheap, really, to stop fighting the Time Lords and just give in, so the Doctor spends most of his time trying to break their hold on the TARDIS. He almost succeeds–only to be back in their grip again. Jamie doesn’t really mind, though, because, as he says, it’s not as if ye could pilot the TARDIS before anyway.
So the pair has many more crazy adventures saving the universe, the world, and occasionally just a few people that the Time Lords deem important enough for intervention. They maintain their dynamic of easy bickering when relaxed and clinging when scared and if time gives Jamie a few more lines around his eyes and lets grey seep into the Doctor’s hair, well, who’s noticing?
Nothing lasts forever, of course. Someday the Doctor will be called back and have to regenerate and face his exile. Someday Jamie will be separated from him. But for now, they’re together. And that’s all that matters.