This is the premise Archibald sent me for the mSRP as part of his official application which was submitted after the mSRP competition: Archibald and criminula, feel free to edit this post at any time.
Task Force Theta is an off-the-books, black ops unit operating on behalf of Starfleet to carry out actions which could never be publically admitted to and it's true leaders remain under a veil of mystery. The USS Atlantis is dispatched to track down and investigate a seemingly rogue group of Starfleet officers who have been running their own agenda across the Alpha Quadrant. However, the clandestine nature of the operation threatens to unravel a long running conspiracy.
Soooooo, Section 31, anyone? :P