Flynn is almost certain to face other charges, unless he turns full state's witness for Mueller. This one charge is also an admission of guilt for violating the Logan Act, but he hasn't been charged with that yet. So Mueller still holds a lot of leverage with Flynn. More importantly, he has implicated another senior official in the Trump campaign as violating the Logan Act, but the identity still remains a secret. The problem for the Trump administration, is that they don't know what Mueller knows or who among them is next. That may soften them up a little when it comes to cutting a plea deal, just like Flynn did. Flynn has pleaded guilty to a felony. Who will be next?
It is impossible to say what kind of chaos Trump will unleash as Mueller closes in on him. My guess is that he will remove Sessions and use the Federal Vacancies Reform Act of 1998 to appoint a replacement, who will then fire Rosenstein and Mueller. The trick is to find someone among his congressionally approved appointments to take on that lightning rod task. It is also possible that presidential pardons will start flying around for his family and loyalists. That would be political suicide for Trump, who would likely be impeached, but he isn't the world's greatest strategic planner. Nixon struck a deal to get himself pardoned. I don't know if Pence will be willing to do the same for Trump. He could give Trump a verbal assurance and then turn his back on him. After all, Trump himself makes those kinds of promises all the time.
Another alternative to having Rosenstein replace Sessions is that Trump could do a recess appointment when the Senate leaves for its holiday.