Ashore, Route commanded the Navy Warfare Development Command (NWDC). From 9 July 2003 to 12 August 2004, he was the 50th officer to serve as President of the Naval War College since the colleges founding in 1884. During his tour as president, he sharpened the colleges focus on mission and relevance; initiated research, analysis, and wargaming to address key operational concerns of the U.S. Navy such as ballistic missile defense and antisubmarine warfare and established the Halsey Scholars, an advanced research program for selected students; and facilitated discussions between retired Soviet Navy officers and their American counterparts on Cold War naval history. Route assumed his duties as Naval Inspector General in August 2004 after leaving the presidency of the Naval War College. His other flag assignments included two tours on the Chief of Naval Operations staff, first as Director, Politico-Military Affairs Division (N52) and later as Director, Navy Programming Division (N80), where he developed and prioritized a multi-year spending plan for the Navy's $80–$100 billion annual budget.