As United States involvement in World War II intensified, Motley joined the U.S. Navy in 1944 and was sent to the Great Lakes Naval Training Station. There he played for the Great Lakes Navy Bluejackets, a military team coached by Paul Brown, who was serving in the Navy during an extended leave from his job as head coach of The Ohio State University's football team. Motley played fullback and linebacker at Great Lakes, and was an important component of the team's offense and defense. The highlight of his time at Great Lakes was a 39–7 victory over Notre Dame in 1945. Motley was eligible for discharge before the game – it was the final match of the season and the last military game of World War II – but he stayed on to play. Motley put up an impressive performance, thanks in part to Brown's experimentation with a new play: a delayed handoff later called the draw play.