Captain Walsh then returned to HSL-41 in 1998 to serve as an Instructor Pilot in the SH-60B Fleet Replacement Squadron. In 2000, Captain Walsh was selected to attend the Seahawk Weapons and Tactics Instructor Course. Following graduation, he reported to the Saberhawks of HSL-47. During this tour, Captain Walsh was a member of the first Carrier based LAMPS MK III detachment in USS CONSTELLATION (CV 64) and deployed to the Arabian Gulf.
Captain Walsh next reported to the Scorpions of HSL-49 and served Officer-In-Charge Detachment FIVE deployed aboard USS VALLEY FORGE (CG 50) in support of Operation IRAQI FREEDOM. Captain Walsh later served as the Squadron Operations Officer.
In March 2004, Captain Walsh was ordered to the Naval War College, Newport, Rhode Island where he earned his Masters of Arts Degree in National Security and Strategic Studies. Following graduation, he reported to United States Strategic Command in Omaha, Nebraska. There he served as Chief, Strategic Mobile Communication Center Management Branch under the C4I Systems Directorate.
In 2009, Captain Walsh became the first Commanding Officer of the Spartans of HSM-70. Following command, he reported to Director of Naval Air Warfare on the OPNAV staff working as the SH-60B/MH-60R Requirements Officer. Captain Walsh took command of the HSM-40 Airwolves in May 2012 serving until October 2013. Captain Walsh has accumulated over 4,000 flight hours in naval aircraft. His personal awards include the Defense Meritorious Service Medal, Meritorious Service Medal (two awards), Air Medal (Strike/Flight), Navy and Marine Corps Commendation Medal (four awards), the Navy and Marine Corps Achievement Medal (three awards) and various unit, campaign and service medals.