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.

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.

[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.

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.

"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.