IMO I think that Section 31 would go deep undercover, and would allow a reporter to investigate them without worrying about reassigning him. First reassigning him would make him and his associates more suspicious, and second it is unlikely he would uncover them but he could help them discover any evidence they have failed to cover up. Heck maybe Section 31 put him on their trail to cover their own tracks!
OK we have three war criminals and could add dozens more but the PCs will be focused on only one or two trials probably. Now how do the PCs become part of this?
Perhaps they are to transport witnesses to the Trial of the Lady Founder, this could include Cardassians, Vorta, and even Jem'Hadar. Of course some are prisoners and some are guests, but a few need to eliminate other witnesses to protect themselves or the Lady Founder. Plus maybe a renegade Jem'Hadar vessel is coming to stop all the witnesses from reaching the trial to protect their god! And worse there is that rogue Founder on board who is trying to manipulate things to the Dominion's benefit.
Follow up adventures may be that one of the Vorta (or any of them) asks one of the PCs to represent him in his trial! This could be where they learn of the true extent of the actions of the Vorta Commander who is being held for lesser crimes than he should be.