On September 5, 2005, while serving as Coast Guard Chief of Staff, Allen was appointed deputy to Federal Emergency Management Agency Director Michael D. Brown by Homeland Security Secretary Michael Chertoff, and placed in charge of Hurricane Katrina search-and-rescue and recovery efforts.
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On April 30, 2010, Homeland Security Secretary Janet Napolitano announced that Allen would serve as the National Incident Commander for the federal government's response to the Deepwater Horizon oil spill in the Gulf of Mexico.
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