At the same time, Brig. Gen. Quincy A. Gillmore was assigned the task of overseeing constructing defenses for the railroads in central Kentucky – Gillmore would go on to command the Department of the South, and is remembered for commanding the assault on Fort Wagner, S.C. While in Kentucky, however, he designed and implemented a series of blockhouses to guard railroad bridges, the first being at Paris on the north side of Houston Creek between the railroad and the Cynthiana Pike. Similar forts protected bridges all the way north to Covington.
To protect the vital railroad junction at Lexington, but not the town itself, Fort Clay was built on what was called Constitution Hill just south of the Versailles Road, overlooking the junction (above what is now the Norfolk Southern yards). The fort, a rectangular design oriented north and south, had a magazine, well and drawbridge. Completed in April 1863, it was surrounded by a ditch protected by pointed stakes to repulse a cavalry charge. Armament included eight 20-pound Parrott cannons, a six-pound rifled James cannon, a 12-pound brass howitzer and two 10-mortars.
Initially, the 48th Pennsylvania Infantry was assigned to the fort. Other Yankee units in and around Lexington included the 9th New Hampshire Infantry, 7th Rhode Island Infantry and 47th Kentucky Mounted Infantry.
In June 1864, Gen. Morgan received permission to raid Kentucky with the express purpose of destroying the Kentucky Central. The raiders first captured Mt. Sterling, but quickly left for Lexington on June 10, with the Federals in hot pursuit. That evening, Morgan demanded the surrender of Fort Clay, but was shelled “vigorously” in defense of the rail lines. The raiders were successful in igniting a fire near the Lunatic Asylum (Eastern State Hospital) and the government corral (today’s Corral Street behind Central Christian Church.)
The following day, Morgan left for Cynthiana, with more than $10,000 from the Branch Bank of Kentucky and a number of Ashland’s Thoroughbreds. Two days later, Union Gen. Stephen G. Burbridge defeated Morgan handily at Cynthiana, forcing his retreat to Virginia.
In what was a classic example of “closing the barn after the horses had escaped,” Fort Crittenden was ordered constructed near today’s Breckinridge and Shropshire streets. It would not be fully completed before the war ended in April 1865. Two other earthworks were started at Clay’s Ferry and lower Tates Creek Road, but likewise never completed.
On August 30, 1865, the last Federal troops in Lexington were mustered out.