Essentially, Supreme Sanction is about abuse of power. A clandestine U.S. government agency called Alpha Section is engaged in Counter Terrorism or CT. The government has been cutting back on funding for counter terrorism (you can tell this was made before September 11th, 2001) and the administrators of Alpha Section come to the conclusion that if their agency's funding is ever going to be restored to its previous high level, then the agency is going to have to create a domestic terrorism scare by engaging in terrorism itself.
The movie begins with a helicopter belonging to an alleged terrorist group in Arizona shooting down a National Guard chopper. Another guard helicopter then shoots down the terroristic copter. In the ensuing investigation, the lead investigator starts to come close to the truth about the alleged terrorist group and just who is behind it and Alpha Section reacts by having one of its top assassins, Jenna (Kristy Swanson) kill him off. This assassination not only removes a threat to the agency's agenda, but it also helps further a domestic terrorism scare in the country.
However, unknown to the Alpha Section higher-ups, Jenna became disenchanted with her job once she realized the full implications of the hit. When the agency tasks her to assassinate award winning TV investigative reporter Jordan McNamara (David Dukes), her feelings towards her employers come to a boil and she rescues him from a certain death. Both Jenna and McNamara are subjected to a harrowing chase by terroristic government agents who will stop at nothing to kill them off.
Eventually, they make their way to the secret hideout of the "invisible man" Marcus (Donald Faison) who is a scientific genius of the first order. Marcus helps Jenna and McNamara craft a plan aimed at both eliminating as many government thugs as they can as well as exposing the evil Alpha Section as the out of control agency that it really is.
While the above may sound like a farfetched plot, the way that this movie is executed, it is a well done action thriller and it actually holds up to repeated viewings. The acting is very good especially by Swanson, Faison and Ron Perlman in the role of the chief administrator of Alpha Section. Of all the main actors, only Michael Madsen turns in a poor showing.