Establish a Counter Terrorist Unit that's an elite branch of the CIA that operates under the Department of Defense and answers only to the President. The agency can be overseen by the National Security Council, of which the Secretary of Defense is a part. Thus, the Secretary of Defense can have some legitimate authority over CTU.
Established domestic counter-terrorism divisional field offices in major U.S. metropolitan areas. The purview of CTU will be to investigate the activities of domestic or foreign terrorists inside America's borders and to prevent terrorist attacks. CTU would employee a broad range of people ranging from ex- military (Delta force,Army Rangers,Special Forces & Navy Seals), investigative agents, intelligence agents and undercover operatives to tactical field teams and special agents to oversee unit activities.
CTU would specifically be set up to coordinate activities with the FBI, the Department of Justice, and the Secret Service, as well as local authorities. All operations of CTU would be top secret ("off the books") to allow for a broad range of counter terrorism techniques, giving agents the freedom to do what ever it takes to secure and protect American interest..