In 1982, Morin received a Direct Commission in the Naval Reserve. In 1983, he entered active duty and attended the Naval Undersea Medical Institute in Groton, Connecticut. He was designated as an Undersea Medical Officer in 1983. He joined the crew of the USS HENRY M. JACKSON (SSBN-730) Precommissioning Unit at the Electric Boat Company Shipyards in Groton. He remained aboard as Medical Officer for both Blue and Gold crews until 1985 when the ship arrived at its homeport in Bangor, Washington. During his tour aboard the USS HENRY M. JACKSON, Morin qualified as Diving Medical Officer, and also received his "Dolphins" as a qualified Submarine Medical Officer.
Morin then entered Flight Surgeon training at the Naval Aerospace Medical Institute (NAMI) in Pensacola, Florida. He received his "Wings of Gold" as a Naval Flight Surgeon in 1986, and remained on the staff at NAMI as Flight Surgeon/Diving Medal Officer until 1989. While at NAMI, he received his Masters of Public Health degree from the University of Alabama at Birmingham. He then left active duty and entered private practice in occupational medicine in Jacksonville, Florida. He remained in the Naval Reserve, and drilled with the United State Marine Corps with the Third Force Reconnaissance Company in Mobile, Alabama.
In August 1990, he was recalled to active duty during Operation Desert Shield, when he was assigned to Branch Clinic, Naval Air Station Pensacola as a Flight Surgeon. Morin volunteered to reenter active duty, and was assigned to Administrative Support Unit, Bahrain, as Diving Medical Officer/Flight Surgeon during Operation Desert Storm and during the post-war build-down period. In 1992, Morin rejoined the staff at NAMI, initially as Special Projects Officer. He was named the Director of Warfare Specialty Programs when NAMI became Naval Aerospace and Operational Medical Institute (NAOMI). In 1995, Morin entered the Residency in Aerospace Medicine at the Naval Aerospace and Operational Medical Institute. He completed the residency in 1996.