While the Navy has its own internal organization, it is a component of the much larger Department of Defense (DoD). How these two elements of national defense interact is complex and not always clearly understood.
Joint Chiefs of Staff
DoD is headed by the Secretary of Defense (SecDef), who answers directly to the President of the United States (POTUS), and he or she is assisted by a senior military officer, known as the Chairman of the Joint Chiefs of Staff (CJCS), who can come from any of the services. The senior military officers of each service (Navy, Marine Corps, Army, Air Force, Space Operations, and the National Guard Bureau) serve collectively as the Joint Chiefs of Staff (JCS).
The CJCS (with the assistance of the other Joint Chiefs) serves only as a principal advisor to the President, National Security Council, and SecDef. At SecDef’s direction, the CJCS may issue directives to operating forces, but these directives are always issued with the understanding they originated with SecDef, not the CJCS.