Here's what happened: After the all the sincere promises and commitments, Jamie in a duel either kills Black Jack or renders him incapable of siring children. But we know, based, on what we saw at the beginning of this season, that Black Jack's descendant Frank is still very much alive in the 1940s. How could that be? Here are some possible explanations:
1. Frank in fact now doesn't exist in the future. But if we have a single time-line universe, that would mean that Claire should have just popped out of existence in 1700s France, since she never would have been there in the first place had she not married Frank in the 1940s. Or, we could have a multiple time-line universe, in which Claire from universe-1 traveled back in time, and set in motion the whole series of events we've seen in these first two seasons, culminating with Black Jack not impregnating anyone, leading to a universe 2 with no Frank and therefore no Claire in the past. This is metaphysically possible, but so far, it looks as if Outlander subscribes to the single time-line universe. So let's look at other possibilities.
2. Black Jack already impregnated Mary, unbeknownst to everyone including the audience, because it happened off-camera. This is not likely, given what we've seen of Mary. If it happened, Mary would have had to been drugged, and unaware or with no memory of this rape. Still unlikely, though with redcoats popping out of closets with no warning, you never know.
3. Frank in fact is a descendant of Mary's relations not with Black Jack but his younger brother Alex. We've already seen that she likes him. This would mean that Frank's genealogy got it a little wrong - either by accident or because someone - maybe Claire later on? - deliberately changed it for some reason to show Jack not Alex as the ancestor. Or, maybe Jack survived the sword thrust, marries Mary, but can't have children, and Mary sleeps with Alex, and they conceive Frank's ancestor. That would account for Frank's genealogy.
That last configuration strikes me as the most likely. But knowing Outlander, it will likely come up with a twist I haven't thought of, which is what makes it so much fun (and, again, I haven't read the novels).
See also Outlander 2.1: Split Hour ... Outlander 2.2: The King and the Forest ... Outlander 2.3: Mother and Dr. Dog ... Outlander 2.5: The Unappreciated Paradox
And see also Outlander 1.1-3: The Hope of Time Travel ... Outlander 1.6: Outstanding ... Outlander 1.7: Tender Intertemporal Polygamy ...Outlander 1.8: The Other Side ... Outlander 1.9: Spanking Good ... Outlander 1.10: A Glimmer of Paradox ... Outlander 1.11: Vaccination and Time Travel ... Outlander 1.12: Black Jack's Progeny ...Outlander 1.13: Mother's Day ... Outlander 1.14: All That Jazz ... Outlander Season 1 Finale: Let's Change History
Sierra Waters series, #1, time travel