In 1848, at the age of 14, Cary entered the U.S. Navy as an acting midshipman. For eight years, he alternated between duty at sea and attendance at the Naval Academy at Annapolis, Maryland. His service took him to the Mediterranean Sea and along the eastern seaboard of the United States, but he tried and failed three times to pass the final examination for graduation from the Naval Academy. Finally, in 1856, he resigned from the Navy in disgust. With no training or education other than his sea duty, in 1860 he joined the Army under the assumed name Mason Howard.
Mason Howard was immediately shipped off to the Oklahoma Indian Territory to fight Comanches. The Civil War soon followed and with Texas seceding from the Union, all U.S. troops in the Indian Territory were withdrawn to Kansas. Carter, now a corporal, and his unit were placed under General Nathaniel Lyon. At the Battle of Wilson's Creek, near Springfield, Missouri, in August 1861, General Lyon was killed and Carter was left severely wounded in the leg. Still using the assumed name of Mason Howard, he accepted a commission in the regular U.S. Army in the spring of 1862. A proven Indian fighter, the Army shipped him off to the New Mexico Territory to fight Indians. Indian fighting and frontier duty remained his occupation for the next 25 years. He took back his family name in 1869, thereafter calling himself Mason Carter.
In 1876, Carter, now a first lieutenant, and his regiment were placed on duty in Montana. In September 1877 they were called on to cut off the flight from Oregon to Canada of the Nez Perce Indians under Chief Joseph. Carter, with a company of about 20 mounted infantrymen, joined a column of the 5th U.S. Infantry under the command of Colonel Nelson Miles. Carter's unit intercepted the Indians at a place called Bear Paw Mountain on September 30. Miles ordered a direct attack on Chief Joseph's camp while another force attempted to encircle the Indians and cut off their retreat. The first attack failed, and Miles decided to cut the camp off from its water supply. To prevent Indian access to a nearby creek, Carter was ordered to lead his dismounted company of 17 men into their camp. This attempt also failed. In this attack, under heavy fire, Carter lost six of his men. The Nez Perce surrendered four days later. Miles went on to a distinguished career, ending up as commanding general of the Army. In 1894 he endorsed an award of the Medal of Honor to Mason Carter for "most distinguished gallantry in action against the Nez Perce Indians at Bear Paw Mountain, Montana, on September 30, 1877, in leading a charge under a galling fire in which he inflicted great loss upon the enemy."
In 1878, Carter was promoted to the rank of captain, and in 1894 he was given the brevet rank of major. Carter continued on active duty until his retirement in 1898. After retirement, he was professor of military science at the University of the South at Sewanee, Tennessee, for 10 years, before moving to California. He died in San Diego in 1909 and was buried at the Post Cemetery at Fort Rosecrans on December 11, 1909.