^I think what we were being shown was that Foster had cured the more recent viral strain, and Jones destroyed the evidence of his success.
In general, I'm tired of dark'n'gritty as a storytelling style, since it's been done to death by this point. But I have to admit, the dark twists last week were really powerful for me and got me more intrigued by the show than I have been up to now. Because it's just so well-done and striking. We've been given half a season to get to know Jones as someone who's eccentric but noble in her intentions, someone we should trust as our heroes' guide through their experiences, and now the rug has been pulled out and we see she's the dangerous, lying fanatic she accused Foster of being. And yet it makes perfect sense in terms of what's been set up before. She's been telling us all along that she expects their entire timeline to be erased — and now we see the horrible ramification of that, since it means she feels entitled to do anything, no matter how brutal, and convince herself that it's okay because she's going to make it all unhappen later on. I love it when a story hides something in plain sight and then reveals it like that. Also, seeing Ramse and Cole turn on each other is powerful since we've gotten so invested in their friendship, and since their reasons make sense.
Dark'n'gritty first caught on because it was such a striking exception to, and subversion of, what had been normal in the past — for instance, when The Dark Knight Returns and Watchmen turned comics on their ear by showing the darker ramifications of superhero stories. But then everyone else started copying those successes, and it wasn't exceptional or subversive anymore, just imitative and fashionable. Just being dark for its own sake isn't enough; light or dark, what's important is to have a meaningful story to tell and to tell it well.
And I think what we're seeing here works as subversion. We've all seen stories about time-travelers trying to undo post-apocalyptic futures, and we're conditioned to root for them, whether it's Kyle Reese or Marty McFly or Kitty Pryde (or Wolverine in the movie). So we've been rooting for Cole and Jones, because it's the formula we're used to. But now the show is telling us, wait a minute, maybe using time travel to undo the apocalypse is the wrong answer. Maybe we've been rooting for the wrong side and ignoring the darker ramifications of the trope. And that is not imitative, that is fresh and subversive and fascinating.