Have al Qaeda spent their time since 9/11 infiltrating the armed services, businesses and science academies using sleepers?

I ask this in regard to the incidents in Afghanistan and America this week and the scientist at Cern being arrested, is this al Qaeda intend to continue the fight against the West?

If it is, I fear for honest, law abiding Muslims living and working in Britain and America, where they will be looked on with distrust and fear leading to witch hunts akin to those Joseph McCarthy's undertook with the communists in the 50's.
Is this their plan, to take terrorism to the next level where people distrust one another enough to turn on them or accuse them of things that they have no dealing with.