In February 1862, Union Gen. John Pope, then stationed in central Missouri, was placed in command of the 20,000-man Army of the Mississippi and ordered to advance on Island #10 and New Madrid. On February 28th, Pope and his men left Commerce, MO and marched south along the Sikeston Ridge through swamps, lugging supplies and artillery, reaching the outskirts of New Madrid on March 3rd and laid siege to the city. For a successful advance, Pope had to cut off routes of supply. By capturing New Madrid, Pope could bring the river under his guns and prevent any enemy supply boats from reaching Island #10 from below.
The Confederates had incorrectly assumed that Pope would not be able to haul heavy and cumbersome siege guns along the miry roads to the Federal entrenchments, which faced the two Forts of Bankhead and Thompson and the Confederate gunboats that protected New Madrid's position. It required 10 days of herculean effort, but on the 12th, the Federals succeed in dragging the four 128-pound siege guns, three 24-pounders and an 8-inch howitzer on huge four-wheeled sling carts to New Madrid and they set about in earnest to shell the forts and the fleet of gunboats.
At dusk Colonel James Morgan's brigade of Paine's division advanced advanced to within eight hundred yards of Fort Thompson. Throughout the evening one regiment worked feverishly on the gun emplacements and trenches, while the other stood guard. The men piled fence rails lengthwise, lapping the ends over and covering them with dirt.
By 3 am the Federals had completed two redoubts with flanking rifle trenches for two regiments. Captain Joseph A. Mower, with two companies of the of the 1st US Infantry, manned the siege guns. The 10th and 16th Illinois were assigned to the trenches, supported by Bissell's engineers. Seven companies of the 2nd and 3rd Michigan Cavalry anchored the far right, beyond the breastworks. The 51st Illinois was positioned on the extreme left flank along the wooded slough that stretched from the river. Slack's brigade moved into a cornfield to the left of Cumming's regiment. Stanley's Ohio division, backed by a dozen field guns, moved in the rear of the main line of battle along the road. More than ten thousand men were deployed to support the siege batteries, with Hamilton's division and Palmer's brigade in reserve.
At dawn on March 13th, a deafening roar jolted the Confederates, followed by a thunderous cheer throughout the Union army. The Confederates were taken completely by surprise.
Unable to hold New Madrid against siege guns, the Confederate commanders ordered the evacuation of the gunboat and their positions at Forts Bankhead and Thompson during the night in the middle of a rainstorm with much confusion. The next morning the Federals quickly occupied New Madrid and entered the deserted forts.