[3] After the start of the American Civil War McLaughlin enlisted in the 2nd Regiment California Volunteer Cavalry September 10, 1861, as a captain.
McLaughlin may have had prior professional military experience in the cavalry arm, (possibly in the antebellum U. S. Army), for one of his superiors, Assistant Adjutant General, Lt. Col. Richard C. Drum mentions him in his report of his tour of inspection of the District of Southern California: At Kline's ranch I found Captain McLaughlin's company, Second Cavalry.
The portion of the company at this station I found admirably instructed in all their duties (excepting their clothing, which is very bad), and in good condition for active service.
"[5]McLaughlin was soon thereafter ordered to Fort Yuma to face a general court marshal for "cruelly beating and maltreating" Private Michael Burke, formerly a member of his company.
[6] On June 6, Lt. Col. George Spafford Evens under orders to organize an expedition to deal with the Indian rising in the Owens Valley, asked headquarters for a fully manned and mounted Company D, and an officer to command it.
In an attempt to control subversion of the Union cause in the secessionist hotbed of Visalia, on the orders of General George Wright, McLaughlin moved his company and another in October 1862 over the Sierra Nevada Mountains from Owens Valley in four and a half days to take command of Camp Babbitt.
[8] On December 12, three men from Visalia rode in front of a dress parade of the garrison and cheered for Jeff Davis, prompting McLaughlin to order their immediate arrest.
Because settlers of Keyesville had appealed to the Department of the Pacific, orders included the instructions: The captain will halt a few days in the upper end of the valley, where the difficulties are said to exist, and investigate the matter, and if the position of the Indians should be found as favorable as represented, if deemed advisable will give them battle.
[11] Also on May 14, 1863, several natives who had remained hidden near the Owens River were captured by Captain Noble's men, and finding that they would not be harmed, but that they would receive food and clothing, and being informed through the interpreter that Captain McLaughlin came to make peace, they were prevailed upon to conduct the troops to where they supposed a large party belonging to Joaquin Jim was encamped and where they could be surrounded.
McLaughlin reports of how he conducted the march: ... upon the evening of July 10, 1863, I had the Indians assembled upon the camp parade ground, where, as they passed by file, they were counted and found to number 998.
I then caused them all to be seated except the chiefs, whom I called to the center of the parade ground, and there announced through the interpreter, José Chico, the orders with regard to their removal.
Seeing that there was no avenue of escape they quietly submitted, Captain George remarking, "American capitan sabe mucho, Indian poco."
The night passed off quietly, and on the morning of the 11th the rations and as many of the women and children as could be were placed in the wagons, and the whole, guarded by about seventy men, composed of detachments of Companies G and E, left Camp Independence.
I am satisfied that had I crossed the desert many lives would have been lost from want of water, and that great suffering at least has been avoided by the route through Walker's Basin.
McLaughlin was also ordered to establish a camp for the summer occupied by one company, nearby or on the South Fork of Kern River, to protect to the whites residing there and in the country known as Owen's Lake Valley.
On August 6, 1863, McLaughlin left Fort Independence with Companies D, E and G for his new post, by a 250-mile march via Kern River, Hot Springs Valley, Walker's Basin, Agua Caliente, the Sinks of Tejon, Sebastian Reservation, and Canada de las Uvas, arriving at Fort Tejon on the 17th of August in eleven marching days, resting one day at Hot Springs Valley for repairs.
[16] The General Court Martial convened at Camp Babbit, Visalia, California, convicted McLaughlin of Conduct unbecoming an officer and a gentleman.
Specifically he was charged: Despite his conviction, all the members of the court, in view of Captain McLaughlin's high reputation, and in the belief that his conduct was owing to a misconception of his duties and accountability as Acting Assistant Quartermaster, signed a recommendation to the reviewing authority for the favorable consideration of the case.
[17] The disability resulting from his dismissal from the Union Army was removed by order of the president of the United States, October 23, 1867,[4] due to the reason that: ... although it is evident Capt.
[2][20] Four years after his divorce, McLaughlin became a doctor, studying at the University of California School of Medicine, San Francisco: Toland Medical College, and graduated in 1878.
The September 23, 1884, Daily Alta California, reported M. A. McLaughlin put his name forward for Supervisor of the Eleventh Ward of San Francisco.