In 1978, he reported to his next assignment as aide and flag lieutenant to commander, Fleet Air Western Pacific, home ported in Atsugi, Japan.

Rear Admiral Naughton joined the staff of Commander, Naval Air Forces, US Pacific Fleet in 1983, where he served as Fighter and Airborne Early Warning Training Officer.

Following squadron command, Rear Admiral Naughton reported to Cruiser Destroyer Group FIVE as air operations officer and once again deployed in USS Kitty Hawk.

In February 1987, Rear Admiral Naughton began Navy Nuclear Power Training, and reported to USS Enterprise as executive officer in October 1988.

This included the first application of radio frequency tracking tags for military cargo and distributed in transit visibility by customers.

From 1998 to 2000, Naughton served as commander, Carrier Group FOUR/Carrier Striking Force where he trained all deploying battle groups (over 100,000 sailors and marines) within the Atlantic area of responsibility and ensured all commanders were fully prepared for any contingency, had maintenance support, supply infrastructure and the proper skills to fight and win around the world.

He was responsible for coordinating installations and testing with Sea, Air and Space Systems Commands to ensure configuration control and supply support for every aircraft and ship that deployed.

Naughton's last assignment in the Navy was as Superintendent of the United States Naval Academy, an organization of over 4,000 midshipmen and 3,000 support staff with an annual budget responsibility of $220 million.