In late 1861, the Union Army was preparing a large invasion force to take the war not only to the Outer Banks but to all of eastern North Carolina. Gen. Ambrose Burnside was placed in command of this new force and Flag Officer Louis Goldsborough would command the naval forces. The first objective of the campaign was the capture of the Confederate stronghold on Roanoke Island. After this was taken, virtually the entire coast of the state would be open to Federal attack. General McClellan's orders to Burnside outlined the Union strategy:
The commodore and yourself having completed your arrangements in regard to Roanoke Island and the waters north of it, you will please at once make a descent on New Berne…you will once throw a sufficient force upon Beaufort and take the steps necessary to reduce Fort Macon and open that port…you will endeavor to seize the railroad as far west as Goldsborough…A great point would now be gained …by the effectual destruction of the Wilmington and Weldon Railroad.
On January 7, 1862, Burnside created the new Department of North Carolina, which was made up of 15,000 men divided into three brigades under generals Jesse Reno, John G. Foster, and John Parke. The three brigades loaded onto transports on the grounds of the Naval Academy at Annapolis and started south. Terrible storms greeted the vessels off the coast, causing the fleet to scatter. On January 26, 1862, the weather cleared and by February 4, the Federal fleet began to cross the bar into Pamlico Sound and head for Roanoke Island.
North Carolina officials quickly realized that Roanoke Island was the key to the state, but could do virtually nothing as the military situation on the coast was now in Confederate rather than state hands. Pres. Jefferson Davis thought it "highly inexpedient" to take away troops from Richmond and send troops to Roanoke Island. As a result, at the time of the attack, only a little more than 1,400 troops were on the island to fight 15,000 of the enemy.
In August 1861, the Confederate Department of North Carolina was created with headquarters at Goldsboro. North Carolina native Gen. Richard Gatlin assumed command, only to have it subdivided by the Confederate government,, with Roanoke Island placed under the command of Gen. Henry Wise ,a Virginian. Wise commanded Forts Bartow, Huger and Blanchard. In the middle of the island, the Confederates had built an 80-foot redoubt protected on the flanks by a swamp and trenches. The island's defenders consisted of the 31st North Carolina Troops, the 8th North Carolina State Troops, and the 49th and 59th Virginia. General Wise, sick from pneumonia, was in Nags Head when the Union forces arrived off Roanoke Island on February 7 and was unable to make it back to the island. The command of the island fell to Colonel Shaw of the 8th North Carolina State Troops.
As the Union Navy entered Croatan Sound, the vessels of the Mosquito Fleet took position just north of the island and prepared to block the entrance into Albemarle Sound. The Union ships began to land troops near the middle of the island and just below the Confederate works. Some of the Union ships bombarded the enemy forts, but much of the fire became directed at the Mosquito Fleet. Colonel Shaw, seeing the enemy land farther to the south, ordered much of the island's garrison to man the redoubt on the causeway on the center of the island. Most of the Union forces had made it ashore on February 7 and spent a terrible rainy night on land. One Massachusetts soldier wrote:
How we wished our thirty or forty pound loads was somewhere else. Finally at 12 we advanced and in a few minutes set our muddy feet on the sandy cornfield where the fires were. We stacked arms…and built for our company four fires of rails we took from a fence nearby. Putting on our rubber blankets to keep off the rain…we sat down to the fire, took off our shoes to dry them, wrang the mud out of our pants and stockings, stirred up the fire, talked, laughed, smoked and got smoked until morning. It was a consolation to us that our officers were obliged to take it with us.
Early on the morning of the eighth, the Union forces began the march north toward the Confederate defenses on the causeway. General Burnside divided his forces into three segments to attack the powerful redoubt. Foster's brigade was placed in the center of the main road facing the enemy works. General Parke's brigade was to attempt to flank the causeway in the swamps on the right of the Union line while General Reno's brigade was to do the same on the left. At first, Foster was not able to advance much against the impressive Confederate fire from the main redoubt, Fort Defiance. After about two hours of this impasse, Col. Rush Hawkins and the 9th New York made a desperate bayonet charge against the enemy redoubt. Although the attack was repulsed, the position was carried when troops of the 25th Massachusetts emerged from the left where they had forded the swamps and flanked the Confederate forces that had started their retreat north.
Meanwhile, the Mosquito Fleet under Captain Lynch, seeing that the cause on the island was lost, retreated to Elizabeth City. Just before retreating, the vessels under Lynch's command landed reinforcements from the 2nd Battalion North Carolina Infantry, who arrived just in time to surrender. With Shaw's forces heavily outnumbered and with no retreat open since the navy had retreated, Colonel Shaw raised the white flag over his tent as forces under General Reno arrived. The battle was over. Federal losses at the battle were 43 killed, 236 wounded and 13 missing. Confederate losses were 23 killed, 58 wounded, 62 missing. The Federals captured over 2,600 Confederates as well as 3,000 stands of arms. It was a devastating defeat for the Confederates. With Roanoke Island captured, the Union Navy now controlled virtually all of the sounds and Burnside could strike at any point at will. He first looked south to capture one of the most important towns in the state, New Bern. After cleaning up at Roanoke Island and leaving an occupation garrison behind, the Union army set sail once again, heading for New Bern to begin the much anticipated capture of the entire eastern part of the state. The true battle for North Carolina had begun.