Lipton was among the first reporters to be assigned to cover the Department of Homeland Security full-time. He started shortly after it was created, writing stories that examined the challenges associated with the largest change in federal bureaucracy since Harry S. Truman was president, and chronicling the agency's struggle as it spent billions of dollars on flawed airport security screening equipment and ships for the Coast Guard. His assignment ended up taking him to disaster zones around the world, including weeks spend in Mississippi and Louisiana in 2005 in the aftermath of Hurricane Katrina, examining flaws in the government response and waste and fraud in hurricane aid. He was also sent in December 2004 to Banda Aceh, along with a team of reporters from "The New York Times", to cover the earthquake and tsunami there that killed more than 150,000.