He led construction of key embattlements protecting Nashville, Tennessee including Fort Negley and Fortress Rosencrans.

[5] From June 1857 to March 1858, he served as assistant engineer of construction of fortifications at Sandy Hook to protect New York City.

[5] The findings were presented to Floyd in his Memoir on the Dangers and Defenses of New York City, which showed that improvement was needed.

In 1860, Morton was selected by the Navy Department to examine the Chiriquí Province in Central America for the possibility of a railroad across the Isthmus of Panama.

While recovering in Washington, Morton was sent in March 1861 to Dry Tortugas, Florida to act as the supervising engineer for Fort Jefferson.

[4] The construction of these defenses, named Fort Negley, was the second most fortified stronghold only outdone by Washington, D.C.[9] It was built using over 2,700 conscripted slaves and free blacks from a nearby camp.

They were ordered to train in Nashville for a month and on November 29, 1862, Morton was commissioned as Brigadier General of Volunteers,[2] a position which President Abraham Lincoln had promised him.

[4] In late December, about 1,700 men of the Pioneer Brigade would join the rest of the Army of the Cumberland on its march to Murfreesboro, Tennessee.

Around mid-day, the brigade was ordered forward to support Captain James Stokes' Chicago Board of Trade Battery, which was positioned on a small knoll west of the Nashville Turnpike, behind the center of the Union lines.

This repulse helped General Rosecrans buy time as he regrouped stragglers and brought up fresh units to reform the line.

Morton rode to the front of his troops and said, "Men, you haven't much ammunition, but give them what you have and then wade in on `em with the bayonets!"

On January 2, Confederate General John C. Breckinridge attacked the Union left center and was successful in capturing a number of guns.

[14] While Morton and the Pioneer Brigade did not have a large role in the Tullahoma Campaign, their record would be marred by some incidents that occurred, including drunkenness among the ranks.

[2] During the Battle of Chickamauga, the Pioneer Brigade fell into the wrong place again, this time in front of retreating Union troops.

[5] Morton returned to the field in May and served as the Chief Engineer in the IX Corps under General Ambrose Burnside.

[2] On June 17, 1864, during the Second Battle of Petersburg, Morton was surveying the area in front of General Orlando B. Willcox's division, which was about to attack, when he was shot in the chest and killed.