The answer to the question of "who's in charge?" during a major disaster in the United States is no one person or agency is ever in charge of all aspects of responding to a catastrophe whether it be an attack similar to 9/11 or a natural disaster such as Hurricane Katrina. When the founding fathers signed the Declaration of Independence and later established the Constitution, one of their fundamental objectives was to ensure that no one person was ever "in charge" in the United States. The founders set up numerous roadblocks to central power by spreading power and authority within and across multiple levels of government and directly to the people. It is a masterpiece in limited government, but it also raises serious challenges when a major domestic crisis hits.
It is odd that we should expect a federal democracy to suddenly pivot into a quasi central dictatorship during major disaster operations. Attempts to centralize power often create more problems than they solve. The post Katrina expansion of the President's power to federalize the National Guard during a natural disaster or other emergency without the Governor's consent, outside those already covered under the Insurrection Act, was later repealed because that expansion actually blurred the lines of authority between the President and the Nation's Governors in terms of who would manage the Guard in such circumstances.
In truth, many confuse their desire for someone to be in charge with a need for someone to provide leadership. On September 11, 2001 Mayor Rudy Giuliani exhibited leadership and led the city's response, but was no more in charge of the National Guard troops any more than President Bush was in charge of the fire fighters at Ground Zero or New York Governor George Pataki was in charge of the FBI. On the grounds of the Pentagon that day, the incident commander was not the Secretary of Defense or a general or an admiral, but was instead the local Arlington County Fire Chief. However, this did not give the fire chief command authority over U.S. troops on the scene. The better question to ask is how do we integrate different agencies from multiple levels of government to effectively respond when a major crisis hits?
Both the National Incident Management System (NIMS) and National Response Framework (NRF) are the chief mechanisms by which the U.S. seeks to overcome its fragmented, federal system of government and evolve into a coordinated response to major disasters. Structures such as unified command and incident command help different agencies and levels of government achieve integration. However, they do not create a system of unitary command whereby a single chief executive wields command authority over all aspects of an incident and then delegates through directives, such as the National Command Authority for the purposes of war fighting. Mayors don't work for Governors and Governors don't work for the President, etc.
Answers to critical questions such as who is in charge of which branch of a given level of government, and which agency has the responsibility for a given objective and who is supporting that lead agency during a crisis, will vary depending on the nature of the incident and where it occurs. The principles and systems outlined in the NIMS and the NRF are designed to make the process of integrating the activities of those agencies a much smoother one, but it will rarely be seamless. Federalism is intentionally difficult and disasters are always chaotic. However, the more training and testing around these systems from tactical operators up to chief executives the better. In addition, within each level of government every effort should be made to clarify roles and the chain of command to ensure that responsibilities within and across agencies are crystal clear on the day of a disaster.
Intergovernmental roles and responsibilities are among the most misunderstood aspects of disaster management in particular and homeland security in general. To ask repeatedly "who's in charge?" is to fundamentally misunderstand our federal system. Rather than trying to find an omnipotent commander where there is none, it is more appropriate to provide leadership and reach a clear and valid understanding of roles, responsibilities and capabilities across levels of government to improve our nation's response when the next major disaster inevitably strikes.