X-Men: After the Chaos is a movie based RPG, taking place after X-Men: The Last Stand, although we have made a few changes to continuity for the sake of sanity.
The United States Government had become worried about the potential power and danger of mutants. In response, they began to debate a new bill that would require all mutants to register their powers and abilities. Because of this, Magneto had decided to to use his knowledge and technology to turn some of these government officials into mutants themselves, thereby changing their minds on any anti-mutant legislation. Charles Xavier's X-Men stopped Magneto from accomplishing his plan. The result however was the opposite. In reaction to his plot, the United States Senate voted approval of the Mutant Registration Act, and sent it to the United States House of Representatives. for the necessary vote.
Later on, Magneto's associates attempted an assassination of the President of the United States. This act was yet again to prove a point. "Aggressiveness towards mutants would lead to aggressiveness from mutants." This act actually made it possible for a Mutant-hater, General William Stryker, to convince the President that mutants were a threat. General Stryker attacked mutant kind and attempted to destroy them all due to his mutant son killing his own wife. The X-Men foiled General Stryker's plot and then convinced the sitting President that mutants were not his enemy. Jean Grey apparently sacrificed herself to help her teammates escape.
A while after her apparent death, it became clear that after seeing the anguish Jean Grey felt over the loss of her friends, the Phoenix forced sacrificed itself to bring back the woman and her lover. However, when Scott Summers came to the place of Jean Grey's apparent death, the Phoenix lashed out and apparently killed him Later on, when the professor tried to force the Phoenix identity back into dormancy, it lashed out and lead Jean Grey to kill the professor.
Later, a seeming cure for mutation was discovered. It is later revealed that this cure is being manufactured at a laboratory on Alcatraz island, from the blood of a mutant. Magneto and his Brotherhood of Mutants gathered an army to attack and destroy this cure since the U.S. Government turned it into a weapon to forcibly cure mutants against their will. The X-Men defended the facility and the mutant from which the cure was derived, Leech. The end result of this battle was lots of mutants forcibly cured & de-powered, including Magneto, Leech being alive, Cyclops dead, Professor X dead, and Jean Grey being Dead at Wolverine's claws, at her insistence.
After the events of Alcatraz island, all seemed lost. Charles Xavier, Jean Grey, and Scott Summers were presumed dead, the students were scattered, some taking the ‘cure’ being administered, and the school seemed on the brink of closing. The school reopened with Jean Grey and Ororo Munroe as Headmistresses for those mutants who had not taken the cure.
The Mutant Registration act was on the back burner in light of the cure, but once the source of it, a young boy named Leech, was removed from their prison, scientists once more scrambled to find a new method of disabling the powered. While some politicians continued to tout the MRA, enough opposition kept the Act from ever fully coming into light.
The cure itself was not what it was promised, and after a year the mutant abilities began returning in those who had taken it. After effects were varied, with some of those who were powerless in the face of their mutations having limited bursts of new found control, while others were unable to reach the full potential of the powers they had once had access to. Eventually, the Cure wore off completely, and due to an immunity, could not be applied.
S.H.I.E.L.D. is operating out of their New York City Headquarters. The Avengers are yet to be formed. The X-Men are finally getting their act together after Jean, Scott, and Charles are all found to be alive. Magneto is off somewhere unknown, and Mystique is now leading the Brotherhood in his place.