The expedition was part of Winfield Scott's overall Anaconda Plan, which aimed at closing blockade-running ports inside the Outer Banks.
In August 1861, Major General Benjamin F. Butler and Flag Officer Silas H. Stringham captured Forts Hatteras and Clark guarding an entry point into Pamlico Sound.
Butler and Stringham were able to persuade the Secretary of Navy Gideon Welles to maintain a force at Hatteras Inlet to keep the possibility of further operations open.
The Lincoln Administration did not agree with invading North Carolina from the sea, but General-in-Chief George B. McClellan was in favor of such an operation.
McClellan was able to persuade President Lincoln to authorize the operation and choose Brigadier General Ambrose E. Burnside to lead the expedition.
In January, 1862 Burnside set out from Fort Monroe and rendezvoused with Flag Officer Louis M. Goldsborough at recently captured Hatteras Inlet where the two assembled their forces.
Huger declined to give aid but eventually Wise's reserves and a battalion of the 2nd North Carolina from Norfolk bolstered the defenses.
[5] By the time Burnside arrived, Roanoke Island was guarded by 3,000 Confederate troops under the command of Colonel Henry M. Shaw.
Burnside then returned to Hatteras Inlet and was reinforced by more ships from the navy for his next objective, the railroad town of New Bern along the Neuse River.
[7] Burnside's next objective after New Bern was the terminus of the Atlantic and North Carolina Railroad at Morehead City and Beaufort along the southern end of Pamlico Sound.
While Fort Macon was besieged the Union forces in North Carolina received additional infantry reinforcements, enough for Burnside to organize 6 brigades.
Now in command of two brigades, Jesse L. Reno was dispatched to destroy the Dismal Swamp Canal locks to prevent Confederate ironclads from moving down from Norfolk.
By June 1862, Burnside had occupied Roanoke Island, New Bern, Morehead City, Beaufort and Washington, North Carolina.
Burnside was preparing for a drive against Goldsborough, his next major objective, when he received orders to return to Virginia with any reinforcements he could spare to aid in the withdrawal of General McClellan's forces after being defeated attempting to capture the Confederate capital.