To help defend the San Francisco Bay and Fort Cronkhite, in 1938 Battery Townsley a case-mated battery that mounted two 16-inch caliber guns, each capable of shooting a 2,100-pound projectile 25 miles out to sea would finish construction in 1940. The guns and their associated ammunition magazines, power rooms, and crew quarters were covered by dozens of feet of concrete and earth to protect them from air and naval attack. Battery Townsley would be fired over 100 times, but only for training exercises. In 1948 Battery Townsley would be scrapped for metal and turned into a warehouse, barracks and test facility for future weapons. This battery was named in honor of Major General Clarence P. Townsley, a general officer in World War I.
After WWII and years to follow Fort Cronkhite would still play an important role for the military. The Commando Combat School would be built at Fort Cronkhite to train officers from the U.S. Army, Coast Guard and California State Guard in commando tactics, combat training, and leadership skills. In the 1970s, Fort Cronkhite became the home base for soldiers operating the nearby Nike missile site. During the 70's the Army had now replaced most of the old wood building with new cinder block barracks to home the personnel manning the Nike Missile sites. By 1974 Fort Cronkhite had been deemed unfit for service and along with the Nike Missile sights it was deactivated.