When mutant prosecutions rose, Mystique in her function as a team leader decided that it were safer for the Brotherhood of Evil Mutants to work for the government. In exchange for full pardons, the old Brotherhood offered their services to Valerie Cooper, at that time a United States National Security Advisor. Not entirely convinced of their sincerity, Cooper wanted the team to arrest Magneto, the Brotherhoods founder, as a proof of their betterment. They got a new name (Freedom Force) and a new member (Spiral). Magneto, at this point himself in a state of reformation from his former ways as a criminal, was helped by his new allies, the X-Men, when being attacked at a remembrance ceremony for the Holocaust, but decided in the end to turn himself in to make up for his former crimes.
Freedom Force were created by Chris Claremont.
Freedom Force stays fairly consistent for most of it's existence, although members tended to come and go, the core members of Mystique, Blob, Pyro and Avalanche stayed around.
Major Story Arcs
Their next mission had them arresting the Avengers, who had been framed by their embittered former member Quicksilver. Their newest member Spider-Woman wasn't happy about this, so she freed them and thereby became a fugitive from the U.S. government. A little while later, the three WW2 veterans Crimson Commando, Stonewall and Super Sabre, wanting to hunt down and execute criminals, had a run-in with Storm, that ended in their defeat and them turning themselves in. The government determined that the former heroes were still reformable and therefore included in the ranks of Freedom Force.
From there on, they went on a lot of missions of difficult nature, such as upholding the Mutant Registration Act, which led to another conflict with the X-Men. But they also had some heroic deeds, like saving the people of Dallas ("Fall of the Mutants" storyline). Rumors that they were forcing young and potential mutants into training for governmental service led to clashes with X-Factor and the New Mutants, around which time Spiral decided to leave the team.
A while later, when the Commission on Superhuman Activities forced Steve Rogers to resign as Captain America, they found a replacement Captain America in John Walker. The new Captain America, and his partner Battlestar, began working for the Commission and joined Freedom Force. This line-up of Freedom Force battled the Avengers, The Resistants and one of Apocalypse's Horsemen. Eventually, Walker was shot by Scourge and Battlestar left the Commission's employ shortly after.
After that, Freedom Force was set up for some hard times. By request of Forge, they protected Muir Island against the Reavers, but at the cost of Stonewall and Destiny being killed and Avalanche severely injured. That had a big impact on Mystique, which rendered her temporarily incapable of leading the team. Shortly after that, Shadow King possessed Valerie Copper with the intention of killing Mystique, but Valerie was able to resist his influence, which resulted in her injuring herself. Mystique used this moment to switch roles with Cooper, thereby gaining access to Shadow King's circle of confidants. Later on, she played a crucial part in defeating the Shadow King together with the X-Men and X-Factor.
Meanwhile, the remaining members went on a mission in Kuwait during the first Gulf War, where they clashed with Desert Sword. That led to Super Sabre being killed and Crimson Commando so severely hurt, that Avalanche was forced to leave Pyro and Blob behind in order to save Commando's life. This was the end for Freedom Force as a team, even though Avalanche and Commando continued to work for the government as covert op agents. The government then took to another mutant group as replacement: X-Factor.