[2] When the American Civil War broke out, he assisted in raising the 2nd California Cavalry Regiment, serving first as a major under Col. Columbus Sims.

After marching to Fort Ruby, in Nevada Territory, Sims was relieved of his command by the Department of the Pacific on August 19, 1862.

Under Connor's command the 2nd Cavalry served in Nevada and Utah during the rest of the Civil War, fighting various native tribes.

McGarry's executions angered the Shoshone even more, prompting them to threaten to kill any white person they found above the Bear River.

As a popular officer and famed for his role in the Cache Valley victory, McGarry was appointed one of the judges that declared the first of three famous California races between the thoroughbreds Norfolk and Lodi a dead heat.

About 11 o'clock he told the servant to clear out, locked the door and was found early the next morning, December 31, 1867, lying on the floor of his room in his own blood, his throat cut and an open pen knife by his side.

General H. W. Halleck, commander of the Military Division of the Pacific and a large number of other officers of the Regular Army, ex-governor Low and several judges of the state courts attended.