Freedom Force was a Government created team, led by Mystique, under the direct supervision of Valerie Cooper. The one stipulation Mystique had was that the members of the team be pardoned for all previous criminal acts. After Valerie agreed she sent them on a mission to capture Magneto which led them into a confrontation with the X-Men. After the fight Magneto gave himself over to Freedom Force in order to stand trail for his crimes against humanity. After Freedom Force took Magneto into custody Spider-Woman joined the team in order to serve her country.
The next mission that Freedom Force was sent on was to arrest the X-Men in San Francisco. This time however Mystique and Destiny were not with the group and Pyro was left in charge. Under his leadership Freedom Force managed to defeat the X-Men, but when the cops arrived it was discovered that they didn't have the proper paperwork to arrest the group. Outraged, the team left San Francisco and accepted a new mission to arrest Rusty Collins. During the pursuit of Rusty, Freedom Force came into conflict with X-Factor causing them to fight in the populated streets of New York and eventually into the sewers. During the fight Mystique recognized Warren Worthington III and later told the press that the X-Terminators were frauds. Freedom Force then left the battle after Destiny received premonitions of the upcoming Mutant Massacre.
Freedom Force is then ordered to arrest the Avengers and Avengers West Coast and the team arrives at a stadium where the two teams were playing baseball. With an arrest warrant this time Mystique orders the Avengers to surrender. The Avengers refuse and a fight breaks out between all the Avengers and Freedom Force. Freedom Force managed to win the battle and took the Avengers into custody. At a trial some time later the Avengers east and west coast were charged with treason and locked away in the Vault. The members of Freedom Force gloated over their victory, except for Spider-Woman who refused to believe the Avengers were traitors. Finally deciding to do something about she broke the two Avenger teams out of the Vault and set them free. Enraged by their betrayal Mystique asked Henry Gyrich if the Freedom Fighters can pursue the escaped Avengers. Gyrich denies them permission and instead sends Quicksilver to catch them.
Sometime later Blob, Pyro, and Avalanche were assigned to help train the new Captain America, John Walker. During a training session Walker took out Pyro and Avalanche easily, but is taken down by the Blob. A few hours later Walker and Lemar Hoskins the new Bucky encounter the Freedom Force and are ridiculed for their performance in the training session. Then sometime later Crimson Commando, Stonewall, and Super Sabre joined the team in exchange for being pardoned. During their initiation Destiny received a vision of the X-Men's death. In the next few days Freedom Force is introduced to the public while Mystique warned her adopted daughter Rogue of Destiny's vision. Rogue ignored Mystiques warning and went to Dallas with the other X-men. Still concerned with Rogue's safety Freedom Force followed them and tried to arrest the team. Refusing to yield the two teams clash until many of the X-Men are knocked out and Mystique is taken hostage by the entity known as the Adversary, who appeared and began to warp reality. Deciding to work together they saved several civilians from the reality warping affects of the Adversary. During a battle against the hordes Adversary summoned, Super Sabre and Pyro are severely injured and are rushed to safety by Blob and Mystique. Unable to help the X-Men fight the Adversary directly they watch from a nearby cameraman’s van as the building the X-Men were occupying collapsed. Believing the X-men to be due to a spell cast by Forge, Mystique curses him.
Freedom Force is then ordered to protect Forge from the New Mutants; the team encounters the young mutants and defeats them. After the battle Destiny warns the New Mutants of the upcoming Inferno, and then decides to let the kids go. Still in Dallas, Destiny has another vision, this time of Cyclops and Jean Grey coming to confront them. Prepared with this information they wait for the two X-Men. When Scott and Jean finally do arrive they question Freedom Force about their son Nathan. Refusing to give them any information, they get into a fight which ends with Scott and Jean winning. Feeling sorry for the two Destiny gives them information on their son's whereabouts.
Several Weeks later X-Factor defeats the Alliance of Evil and Freedom Force shows up and takes the Alliance into custody. Before they leave they insist that X-Factor register with the mutant registration act. After some discussion X-Factor agrees and signs with phony names. Rusty Collins, who is with them refuses to sign, but gives himself up in order to stand trail for his past crimes. Freedom Forces next assignment was to arrest a group of mutant terrorists known as the Resistants with the help of the new Captain American, John Walker, using a mock trial of Quicksilver to draw the terrorists out. As the Resistants arrive on the scene they spot Captain America and realize it’s a trap, they cause a nearby building to crumble forcing Freedom Force to save the civilians in the building, letting the Resistants get away.
Some time later, Senator Robert Kelly was kidnapped by a drug dealer named Senior Muerte. Ordered to rescue the Senator, Freedom Force arrives on the scene and is assaulted by a team of second rate villains called the Grip. After beating the Grip, the team rescued Senator Kelly and returned to Washington. Freedom Force next arrived on the scene when X-factor defeated Nanny and freed some kidnapped children. Freedom Force told X-Factor that they would take care of the children and that Rusty Collins was cleared and free.
Spiral then sends Blob and Pyro on a mission to register a little mutant girl known as Amanda in a small undisclosed town. As they chase Amanda, trying to catch her they are attacked by Daredevil and are beaten. Spiral then shows up and scolds the two for their blunder. After some time Freedom Force again try to arrest Rusty Collins, but are stopped by both the New Mutants and Skids. After a skirmish with the team Dani is hurt and the New Mutants decide to help her and let Skids protect Rusty. After a few hours of hiding behind Skids force field Freedom Force finally captures the two young mutants.
Later Destiny foresees her own death before Freedom Force is assigned to their next mission. Freedom Force is then ordered to help Forge on Muir Island. Mystique, despite her hatred for Forge agrees. As they arrive on the island they are attacked by a group of cyborg mercenaries called the Reavers. During the battle Mystique sends Destiny away and orders Forge to guard her. Destiny then later tells Forge that Mystique needs him more than she does and he leaves her to join the battle. Destiny then encounters Legion and is killed. The other members of Freedom Force continue to fight the Reavers and Stonewall is killed by Donald Pierce. After Forge rescues his teammates Mystique learns of Destiny's death and swears revenge on Forge for killing both Rogue and Destiny.
Mystique still on Muir Island is confronted by a future version of herself and decides to take some time off to mourn Destiny's death. She then takes Destiny's ashes on a cruise and scatters them out to sea. Elsewhere Blob, Pyro, and Avalanche attack the Avengers and are defeated easily. Later Mystique rejoins the team and sends Blob, Pyro, and Crimson Commando are sent on a mission to find the Hulk in South Carolina. Upon arriving in the small town they encounter the Hulk and one by one are defeated, until Crimson Commando shows his valor by saving a child from some wreckage. The Hulk talks with the Commando for a while and then decks him, knocking him out. The Hulk then leaves Freedom Force where they laid.
After some time Rusty and Skids manage to escape prison in order to stop the Vulture and Nitro from blowing up several city blocks. Freedom Force arrives on the scene and takes the two mutants back into custody. Mystique later questions Skids about the Mutant Liberation Front. Realizing that Skids knows nothing about them she leaves Skids. Later during that day the Front arrives and rescues both Rusty and Skids.
Somehow Freedom Force had made Cable their prisoner and Pyro, Blob, Super Sabre, and the Commando question him about the Mutant Liberation Front. He refuses and the team leaves the room. Cable manages to escape his cell and the members of Freedom Force chase after him. During their chase Super Sabre is almost decapitated by a wire and Cable manages to escape. Later the Freedom Force members search the city for Cable and manage to find him. As Blob, Pyro, Super Sabre, and Commando start to beat Cable up the New Mutants arrive and defeat the four Freedom Force members.
Later Emma Frost sends false information to Freedom Force about Firestar. Determining that she would be a perfect candidate to join the team, they track her down and ask her to join. After refusing a few times the team attacks her. The team then joins forces with Firestar to fight an organization known as the Arms of Salvation. After the battle with the criminal organization they decide Firestar is not "Freedom Force material" and wishes her well on her future adventures.
Sometime late Freedom Force and the Avengers are called in to stop a prison break at the maximum security prison, the Vault. The team confronts several villains such as Hydro-Man, Venom, Mentallo, and the Controller. After the crisis at the Raft was dealt with, Freedom Force returns to their headquarters in Washington.
One night Mystique is shot by Valerie Cooper who is possessed by the Shadow King. Later it is said on the TV that Mystique was in fact dead, but this was untrue. The remaining team consisting of Super Sabre, Crimson Commando, Blob, Pyro, and Avalanche are sent on a mission to Kuwait where they are to rescue a scientist. As they retrieve the professor Super Sabre is decapitated and killed, while Crimson Commando's right arm is cut off. The team then sees their attackers, the Arabian super team called Desert Sword. The two teams clash and during the battle the professor is killed. Deciding that their mission is a bust Avalanche carries the Crimson Commando to a rescue helicopter and leaves Blob and Pyro to fend for themselves. Blob and Pyro were eventually caught and put into jail until the Toad bartered for their freedom if they joined the new Brotherhood of Evil Mutants. After the incident in Kuwait, Freedom Force was disbanded.