A bunch of higher-ups in the U.S. Government don't like the fact that SHIELD and Nick Fury has so much control over the elite superhumans (The Ultimates)
So they create their own super-team; the Thunderbolts. Recruiting from the pool of imprisoned supervillians and unknowns, they're given new identities and a large P.R. budget.
However, they face opposition from other political forces, as well as internal frictions and the traditional dangers faced by superheroes ...