This is the basic idea of the game, its foundation. This may change a little during the course of the story.
Rebuild and start over. Picking yourself up out the ashes and brushing off the dust to face the task of starting from scratch is possibly one of the hardest obstacles ever to confront a person. Discouragement, hopelessness, and grief weave in amongst the setbacks in order to strengthen what is against you. Time is both an enemy and a friend. And time is what the world got.
Ten years ago a secret branch of the government was founded with the goal of better understanding the mutant genome. Like so many other things, however, such a seemingly innocent directive quickly escalated into something dark, cruel and sinister. Mutants were disappearing off the streets and from their homes, being tortured in ruthless experiments for the purpose of comprehension not only for knowledge's sake but for suppression and the harnessing of mutant powers as both weapons. It went so far as to them accomplishing the task of giving normal human beings abilities known only to their mutant brothers and sister.
As it happens during all pursuits of power, the skies darkened and the threat of war crept in. Organizations such as the Brotherhood were not going to stand for these horrors. The X-men tried desperately to keep the peace between humans and mutants while simultaneously putting a stop to the occurring atrocities. In culminated in a conflict that could only end in blood and tears. Death was dealt on both sides. Some mutants were stripped of their powers. And Xavier's School for the Gifted was destroyed.
Over the course of a decade a tentative peace has been forged, one that - as you might have guessed - is not welcomed nor trusted by all. During this time there had been a present need for a haven for mutant children where they could grow, learn, and train. And so a school was founded in Snow Valley, Massachusetts by Emma Frost: the Massachusetts Academy. Meanwhile, Erik Lehnshur has begun plans for a small island nation where mutants can also be safe and protected.
Of course Charles Xavier and his X-men have not been idle either. Despite the hardships that had faced them after the events that had taken their home and their school, the dream and determination was still very much alive. Several months ago they christened a brand new school, build upon the very moral foundation that had started everything from the beginning. Along with the physical Institution, they have also initiated a cyber charter school program to allow children to pursue their academic studies from the comforts of their home (if they are lucky enough to have that) as well as transportation to come to the school for both association and training.
People are starting to grow more at ease as things begin to look up. The talks of peace, however, bandaid the wounds that run deep beneath. The government aid that is being extended mutants and their families is merely balm over the tension that is ever present in a society where two stages of trying to peacefully cohabit their world. The rope holding everything together is pulled taut by the storm pressing against it, waiting to snap. Just a little more pressure, a little more force...or someone to come along with a pair of scissors.