Returning to the Fleet Marine Force in 1985, he commanded two infantry companies and served as the operations officer of Third Battalion, 4th Marines. During this period he commanded the first surface rubber boat raid company in the Marine Corps, and also received the Leftwich Leadership Trophy. In 1988, Brigadier General Allen returned to the Naval Academy where he taught in the Political Science Department. His course work centered on international organizations, regional politics, and intelligence. In 1990, he received the William P. Clements Award as military instructor of the year.
Brigadier General Allen reported to The Basic School as the Director of the Infantry Officer Course from 1990-1992 and was subsequently selected as a Commandant of the Marine Corps Fellow, serving as a special assistant on the staffs of the 30th Commandant and the Commanding General, Marine Corps Combat Development Command. He assumed command of Second Battalion, 4th Marines, subsequently designated as Second Battalion, 6th Marines. This unit served in Caribbean contingency operations in 1994 and in Balkans contingency operations in 1995-1996 as part of the Landing Force of the 6th Fleet.
Following battalion command, Brigadier General Allen reported as the Senior Aide de Camp to the 31st Commandant of the Marine Corps, ultimately serving as his Military Secretary. He commanded The Basic School from 1999 to 2001, when he was selected in April 2001 to return to the Naval Academy as the Deputy Commandant. Brigadier General Allen became the 79th Commandant of Midshipmen in January 2002, the first Marine Corps officer to serve in this position in the history of the Naval Academy.
Brigadier General Allen graduated from the Naval Academy with the Class of 1976 and received a Bachelor of Science degree in Operations Analysis. He is a 1998 Distinguished Graduate of the National War College. He holds a Master of Arts degree in Government from Georgetown University, a Master of Science degree in Strategic Intelligence from the Defense Intelligence College, and a Master of Science degree in National Security Strategy from the National War College.
Brigadier General Allens' personal decorations include the Legion of Merit with three Gold Stars in lieu of four awards, the Meritorious Service Medal with Gold Star in lieu of two awards, the Navy and Marine Corps Commendation Medal with three Gold Stars in lieu of four awards, and the Navy and Marine Corps Achievement Medal with Gold Star in lieu of two awards.