Captain Nathaniel Lyon, aware that the governor had secretly had artillery shipped from the Confederacy to the militia, surrounded the State troops and forced their surrender.

He returned to St. Louis in the spring of 1862 and took over a cavalry regiment, with command of the District of Northeast Missouri, and the special charge of clearing the area of guerrillas—notably, those flocking to Joseph C. Porter.

He spent the summer in pursuit of Porter, who had been ordered into the region to recruit troops to be sent into the Confederacy for training, as well as to generally disrupt Union operations.

However, Harper's Weekly quoted a defender: These measures were severe, but not from the character of General McNeil: he will receive the applause of all earnest patriots for treating treason as it deserves.

But he will bear such calumnies, and live to reap grateful tributes.It was true that Confederate President Jefferson Davis had threatened to execute ten Union prisoners unless McNeil was handed over to the Confederacy, but the threat was not carried out.

The local loyalist paper however supported McNeil: "The madness of rebellion has become so deep seated that ordinary methods of cure are inadequate."

(Palmyra Courier, October 18, 1862) and McNeil himself would respond years later "... cherishing, as I do, the firm conviction that my action was the means of saving lives and property of hundreds of loyal men and women, I feel that my act was the performance of a public duty."

As a pair, McNeil and his nemesis, Joseph C. Porter, illustrate particularly well the horrors of the war and the difficulty of moral evaluation; it seems likely that the culpability of each was minimized by his own side and exaggerated by the other.

During the Battle of Westport, McNeil was relieved of command for "cowardice and failure to attack the enemy" by General Alfred Pleasonton.

McNeil was given the brevet rank of major general of volunteers in recognition of faithful and meritorious services during the war, to date from the day of his resignation.

He was in 1876 commissioner to the Centennial Exposition in Philadelphia, was an inspector in the U. S. Indian service in 1878 and 1882, and at the time of his death was superintendent of the United States Post Office, St. Louis branch.