the term commander in chief refers to the United States president, well there's another commander in chief which is the Commander of United States cyber command
NSA Currently under Admiral Michael S. Rogers
supervision, Originated as a unit to decipher coded communications in World War II, it was officially formed as the NSA by President Harry Truman in November 4th 1952
The National Security Agency (NSA) is a national-level intelligence agency of the United States Department of Defense,
Is responsible for global monitoring, collection, and processing of information and data for foreign intelligence and counterintelligence purposes
The NSA is also tasked with the protection of U.S. communications networks and information systems.[
As any highly classied intelligency agency NSA is surronded by conspiracy theories, worth to mention that even one of the Bitcoins birth theories is related to this agency as mentioned by 
Not only this but many other theories can be found on the Internet, take a look of them .