During the next three decades, he served in the Mediterranean, West Indian, and Home Squadrons as well as on the Great Lakes in Michigan. While serving in Mississippi during the Mexican War, 1846–1848, he participated in Commodore Matthew C. Perry's Mosquito Fleet Campaign and the blockade and siege of Veracruz. He commanded the sloop-of-war Warren from 1854–1856 and the steam tug John Hancock in 1856.
In 1862, Captain McDougal assumed command of the screw sloop Wyoming, in which he cruised in the Far East protecting American merchant ships from pirates and Confederate raiders. On 16 July 1863, he took his ship into the Straits of Shimonoseki to engage shore batteries and three ships of Prince Mori, clan chieftain of the Chōshū. During an hour’s brisk action, Wyoming sank two ships, heavily damaged another and engaged shore batteries.
On 23 December 1869, Captain McDougal assumed command of the South Pacific Squadron. He was appointed rear admiral on 24 August 1873.
Admiral McDougal died at San Francisco, California on 7 August 1882 and is buried at Mountain View Cemetery in Oakland.
