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Not much is known about the NSA in inFamous, but they had an involvement with the First Sons and The Blast. The First Sons were a cult group, trying to advance the human being. NSA Agent John White went undercover in the Empire City branch of the agency, and discovered that their leader, Kessler, was working on a device called The Ray Sphere. The device was to drain the neuroelectric energy out of a crowd of people, and transfer it into an indivudal. On activation, the Ray Sphere would also create a devastating blast, killing thousands of people.
Kessler later gave the Ray Sphere to bike courier, Cole MacGrath. John tried to stop him, but lost him in a red light. The government applied a quarantine, thus preventing John from getting out. John was stuck in Empire City, and it appeared he'd been abandoned. They were later to pick him up, but John died before they could.
During John's time working undercover, they gained massive amounts of information on the First Sons and the Ray Sphere. He put most of this information in messages, called Dead Drops. John would later state that this could mean a second Ray Sphere could be created.
While John White was working in Empire City he maintained contact with NSA agent Lucy Kuo and affiliate Sebastian Wolfe who were working in the New Marais branch of the First Sons. Together these three formed a triangle of double agents who were working in the First Sons on behalf of the NSA