After the Northern Pacific, Bogue served as chief engineer of the Union Pacific Railroad until 1891. Following this, he was also chief engineer on the Western Maryland Railway and headed up the construction of the Western Pacific Railroad through California's rugged Feather River Canyon.
As a consulting engineer, Bogue worked on Columbia River Navigation, Commencement Bay and Grays Harbor, the New Zealand Railway, the New York Department of Public Works, and finally, shortly before his death in 1916, the Greater Seattle Plan.
His "Bogue Plan" was rejected by voters on March 5, 1912 by a 10,000-vote margin. It would have established Seattle's first comprehensive plan and a variety of improvements, including a civic center in the new Denny Regrade area. The civic center was eventually realized five decades later as Seattle Center, more or less in the location Bogue proposed.