It looks like most of the Fulcrum agents may have survived the brain blast from their own experiment, caused by Casey starting up the program. However, the Meadow Branch team leader Brad appeared to have been killed by the mental onslaught - we saw him getting zipped up into a body bag. But as Casey was snarling orders to get the living Fulcrum agents to detention, he had special instructions for Brad's body....
"That one goes to the Agency's morgue. We're not done with him yet."
It reminded me of the ending of the pilot episode for 'Fringe', in which Nina Sharp wanted the memories extracted from the corpse of FBI Agent John Scott, and a little thing like Death wasn't going to stand in her way.
Could the CIA and the NSA have access to the same technology that was developed at Massive Dynamics? BCnU!