There are hundreds of stories out there about how the Scoobies get super-mature after "Chosen" and, in classic know-it-all style, they fix all the old Watchers' Council's mistakes.
Here's the challenge: keep it in character, and have them screw up. Monumentally. None of them really have the administrative skills to run something global, like the Council, anyway; they barely manage to keep their heads above water, most times.
So, what are the possibilities?
How about they decide that the SGC has got to be another Initiative, because, yes, covert government military ac...