A series of new processes and procedures for cybersecurity were put into place this month. They pave the way to better leverage the Defense Department's cyberwarfare capabilities in case there is an attack on the U.S. networks.
Think about the situation where you have a wildfire raging or a major hurricane. The President can sign an order that allows FEMA to organize and coordinate recovery efforts using U.S. military forces. The new procedures adopted for cybersecurity follow similar guidelines.
In this case, DHS would direct the work of the U.S. military.
According to a New York Times article, DHS team will deploy to a military base on Fort Meade, Md where the NSA and the military have instituted the Cyber Command. A team of experts from Cyber Command will be assigned to the operations center at DHS.
Protection of civil liberties will be managed through a team of lawyers.
"Pentagon Will Help Homeland Security Department Fight Domestic Cyberattacks', Thom Shanker, New York Times, October 20, 2010.