Perhaps the two best-known emergencies of this sort in American history have been the Civil War and World War II.
In the Civil War, people in the government believed that the need for community security was paramount. They feared spying and they feared that Southern sympathizers would foment rebellion in the North. For these reasons, they were willing to infringe on individual autonomy by suspending the right to habeas corpus.
In World War II, there was a great fear (in the early part of the war) of Japanese invasion and/or sabotage of the West Coast. People in government believed that community security was threatened by people of Japanese descent. This led to the internment of all people of Japanese descent on the West Coast.
In both of these cases, the balance between individual autonomy and rights and community security was tested.