This would be the X-Men: Blackbirds book I keep tossing out in these roster wishlist threads. While Uncanny X-Men would be a bit of everything, from a mutant Champions to mutant Stormwatch to mutant New Avengers... X-Men would become mutant Thunderbolts. Rogue, Cyclops and Wolverine take the initiative of transforming villains with potential into a successful rescue and crisis prevention team. Along the way, Cyclops is transformed by perspectives outside of Xavier's moral center, and leads the team of ex-villains into actual pro-mutant terrorist behavior.