With the surrender of Fort Henry and Fort Donelson, Tennessee, and the evacuation of Columbus, Kentucky, Gen. P.G.T. Beauregard, commander of the Army of the Mississippi, chose Island No. 10, about 60 river miles below Columbus, to be the strongpoint for defending the Mississippi River. On a peninsula 10 miles long by 3 miles wide, the defenses consisted of a 2-regiment redoubt at New Madrid, and land batteries on a floating battery at Island No. 10. The latter was covered by land batteries on the Tennessee Shore.

Meanwhile, the Union forces in Missouri, previously occupied in the North-central and western parts of the state chasing Gen. Sterling Price, were now under the command of Maj. Gen. Henry Halleck. Halleck put together a plan for collapsing the Confederate western flank, which included the Mississippi River defenses at Island No. 10 and New Madrid. Halleck ordered Brig. Gen. John Pope to move on the Confederate forces at New Madrid. Pope arrived at Commerce, Missouri on February 25 with an escort of 140 men, and by March 1st, Halleck had assembled an army of 12,000 for him to complete the assignment. By March 2nd, his advance pickets arrived at New Madrid and the following day the remainder of the Army of the Mississippi arrived on the edge of town, having marched the 50 miles of Missouri springtime mud in 3 days. The force marched overland through swamps, lugging supplies and artillery.

On March 3, the Federals reached the New Madrid outskirts, and laid siege to the city. Brig. Gen. John P. McCown, the garrison commander, defended both New Madrid and Island No. 10 from the fortifications. He launched a sortie, under Brig. Gen. M. Jeff Thompson, Missouri State Guard, against the Union besiegers and brought up heavy artillery to bombard them.

Upon his arrival, Pope discovered that five Confederate gunboats, under the command of Commodore George N. Hollins, had further reinforced New Madrid. The river, typical of springtime stages was nearly out of its banks, allowing the heavy guns on board the boats to sweep the countryside for several thousand yards ahead of Pope's army. Additionally, his intelligence on the size of the New Madrid garrison was sketchy at best, so a general assault was not ordered.

On March 4, and March 6, Pope ordered a reconnaissance in force on the Confederate positions near town, and pushed the pickets in, but still had very little idea of the size of the garrison. Finally on the 7th, a general demonstration against the Confederate works was ordered. Gen. David S. Stanley's Division was ordered to move on Fort Thompson while Col. W. H. Worthington's Brigade was to move on Fort Bankhead and occupy the trenches. John M. Palmer's 1st Brigade was to support Worthington. The Confederate's discovered the feint and the gunboats opened up on Worthington's men. Now, caught in crossfire between the Confederate gunboats and heavy guns in the forts, the force of approximately 7,000 withdrew from the town without engaging the Confederates. Pope, his Division commanders agreeing, concluded that an all out frontal assault would be suicide and decided to put the garrison to siege. He then telegraphed Halleck for siege guns and kept his command well distanced from the Confederates to await the big guns arrival.

Pope continued with other strategies too.
On March 6, Brig. Gen. J.B Plummer 's Division was ordered 5 miles down river to Point Pleasant, Missouri. Plummer's mission was to set up batteries on the river in order to cut off Confederate supply boats from New Madrid and No. 10. Plummer's men dug in along the riverbank; although the Confederate gunboats attempted to dislodge the Federals with their wooden fleet of gunboats, they failed. Plummer's men riddled the boats with small arms fire and scored several direct hits from their field pieces. The Confederate fleet proved it had little offensive value. The Union siege guns, three 24-pounders and one 8-inch Howitzer, arrived on March 12 and were planted in front of Fort Thompson that night.

On March 13, in the morning, the Federals began returning the Confederate artillery fire in earnest. A daylong artillery battle ensued, and although not terribly bloody, there were total losses on both sides in excess of 100 killed and wounded. The Yanks showed themselves to be good marksmen, dismounting 2 heavy guns in Fort Thompson and scoring several direct hits on the gunboats. The Confederates, not to be outdone, placed an 8-inch ball directly into the muzzle of one of the 24 pounders. Pope ordered an infantry assault on Fort Bankhead by Palmer's Division, however the Confederates discovered the plan and trained the big guns on the hapless Federals. Palmer, an Illinois politician, approached the fort to within about of a mile, and then refused to order the assault. Pope acquiesced to Palmer's decision.
That evening, Stewart, McCown and Commodore Hollins met aboard the Flagship McRae and concluded that the situation at New Madrid was hopeless. Within hours of the meeting, under the cover of a terrific spring thunderstorm, the Confederate forces evacuated New Madrid and crossed over to the opposite bank of the River. The evacuation was botched from the beginning, there were too few transports, the big guns were left unspiked, the caissons and limbers from the field pieces had to be thrown overboard from the transports, pickets were left in the trenches, and bodies left unburied. Overall, it had the appearance of a route rather than an evacuation.

On March 14, Pope's army discovered that New Madrid was deserted and moved in to occupy it. A Union naval flotilla, under the command of Flag-Officer Andrew H. Foote, arrived on March 15, coming upstream from Island No. 10. The ironclad USS Carondelet, on the night of April 4, passed the Island No. 10 batteries and anchored off New Madrid. The USS Pittsburgh followed on the night of April 6.
The ironclads helped to overawe the Confederate batteries and guns, enabling Pope's men to cross the river and block the Confederate escape route. Amazingly, the Federals watched the Confederate transports all night long, but they could not determine if it was an evacuation or reinforcement. The following morning, the Union troops were marched on to the field and Pope prepared for the assault that he had been avoiding. A flag of truce appeared in Fort Thompson from the Confederate pickets who had been left behind. Soon, all of Gen. Pope's army learned that the Confederates had made their escape. Cheers swelled in the ranks, and Pope quickly received his kudos from Halleck for the nearly bloodless capture of the garrison.

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