In 2001, Kelly returned to the United States to join NPR in Washington. For three years, she edited NPR's evening newsmagazine, "All Things Considered". The NPR website described her as a "bad-ass babe on breaking news". In 2004, Kelly launched NPR's intelligence beat. She reported on spy agencies such as the Central Intelligence Agency, the Defense Intelligence Agency, and the National Security Agency. In 2005, Kelly became the first reporter to interview Gary Schroen, the CIA operative who was dropped into Afghanistan in the aftermath of the September 11 attacks with a six-man team and a directive to bring back the head of Bin Laden. In 2006, Kelly broke the news of the CIA's secret decision to disband the unit aimed at searching for Osama Bin Laden. The story caused an uproar and led to the Senate voting on September 8, 2006, to reinstate the unit.