As the USCG Commandant, Loy reacted to the September 11 attacks of 2001. In the short term, he supervised the resumption of sea-borne trade throughout the U.S., after the USCG had shut down most major ports after the attacks. In the long term, Loy led the U.S. delegation to the International Maritime Organization (IMO), and was instrumental in ensuring that the International Ship and Port Facility Security Code was approved and implemented in 2002. The code came into effect in 2004.
On October 23, 2003, Loy was nominated as the U.S. Deputy Secretary of Homeland Security by U.S. President George W. Bush, and sworn in on November 4, 2003. Following the departure of Tom Ridge, Loy filled in as ActingSecretary of Homeland Security from February 1, 2005, until February 15, 2005, when Michael Chertoff was confirmed and sworn into office. Joining the exodus of leadership, Loy resigned as Deputy Secretary, effective March 1, 2005.
On April 7, 2005, the Cohen Group announced that Loy had joined the firm as a Senior Counselor, effective April 18.[5] On August 5, 2005, Loy joined the Board of Directors for Lockheed Martin.[6]
In the fall of 2006 it was announced that Loy was being honored as the first Chair of the Tyler Institute for Leadership at the U.S. Coast Guard Academy. As such Loy has played a significant role in speaking and drawing other distinguished visitors to the Academy. His first class was designed to teach a select group of cadets about the international shipping industry and how it might be secured.
In March 2007, The Washington Post had a feature on Loy and his relation to the U.S. Coast Guard's Deepwater contract, which was awarded to Lockheed Martin in summer of 2002. When asked by the Washington Post if he ever faced improper influence on Deepwater decisions while serving as the USCG Commandant, Loy said: "The question is almost insulting. I will pass on giving you any kind of answer."[6]
In 2020, Loy, along with over 130 other former Republican national security officials, signed a statement that asserted that President Trump was unfit to serve another term, and "To that end, we are firmly convinced that it is in the best interest of our nation that Vice President Joe Biden be elected as the next President of the United States, and we will vote for him."[7]
In July 2022, Loy joined with other former U.S. military leaders in condemning former president and commander in chief, Donald Trump. "While rioters tried to thwart the peaceful transfer of power and ransacked the Capitol on Jan. 6, 2021, the president and commander in chief, Donald Trump, abdicated his duty to preserve, protect and defend the Constitution.[8]
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