How is the Department of Defense run?

Other than the President (who serves as Commander-in-Chief of the armed forces), the most powerful DoD official is the Secretary of Defense. The Secretary is superior to the Joint Chiefs of Staff (the highest-ranking officers from each branch of the military). The current Secretary of Defense is Robert M. Gates, who was originally appointed by President George W. Bush after the firing of Secretary Donald Rumsfeld and was asked by President Barack Obama to continue as Secretary of Defense in the new administration.