I have been planning on running a game where the PCs are superhumans who have only just developed their powers. It turns out that they were engineered by the government to have these powers and put into families that had considerable loyalty to the government. In my case thats the Canadian government, but use whichever one you want.
Basically the idea is to pull your stories out of the headlines in the real world press. Around the time I first thought of this idea was 9/11, so I was gonna have the players go and try to catch Bin Laden. Sorry if I am offending anyone by bringing that whole issue up, thats not my intent.
If you have a group who have been kept away from the real world for awhile then its pretty easy for the Major to tell them anything he wants and if they trust him they should believe it. Then maybe the way they figure out that he is evil is that someone tells them that they are going after the wrong guy. Like make up a terrorist, who is actually an anti-terrorist, have them go after him and eventually they find out that he was one of the good guys.