Seemingly without equal, the Albemarle moved on with impunity, shelling Union forts along the river with her rifled cannons. With the accompanying land army taking ground and no enemy naval support to contend with, Union forces now found themselves hopelessly surrounded, allowing Confederate General Hoke to take Plymouth and the available Union forts. Confederate forces captured Fort Comfort, eventually driving the Union defenders into Fort Williams where General Wessell formally surrendered on April 20th. Prior to its surrender, Confederate President Jefferson Davis had been preparing to evacuate the southern capital of Richmond. Onboard the CSS Albemarle was John Taylor Wood, a nephew to Davis, and it was he that sent word of the Confederate victory. Davis now felt the Confederate lifeline safe for the moment and did not abandon the capital.
The Union Navy now moved more warships in to help blockade Albemarle Sound and the mouth of the Roanoke River. On May 5th, the CSS Bombshell with the CSS Albemarle escorted a Confederate troop carrier - the CSS Cotton Plant - down the Roanoke River to challenge the new blockade. Entering the bay, the Confederate forces came upon four Union warships - the USS Miami, the USS Mattabesett, USS Sassacus, and the USS Wyalusing. Completely outgunned, the CSS Albemarle and CSS Bombshell nonetheless opened fired, targeting the more vulnerable wooden USS Mattabesett. The volley struck one of Mattabesetts two 100-pounder Parrott rifles and wounded six crew. Albemarle then moved on to ram the USS Mattabesett though the Union vessel managed to steer clear of the approaching Confederate ship.
The USS Sassacus steamed into the path of Albemarle and fired a broadside of solid 9-inch (229 mm), 100-pound shot - all of which bounced off Albemarle's casemate iron armor. Sassacus then moved on to attack the CSS Bombshell which, after receiving many hits from Sassacus was, was captured by a Union sloop. USS Sassacus again set her sights on Albemarle at a range of about 400 yards (370 m) but this time decided to ram her. Sassacus reached the Albemarle at amidships, smashing her own ram in the process but embedding it into the side of the Albemarle. Now conjoined, Albemarle gun crew fired two rapid, point-blank rifled shells into her foe, one of them pierced Sassucus' armor and detonating a boiler. The leaking boiler then sent boiling water and steam throughout the internal works of the Union ship, wreaking havoc and injury to the crew. Eventually freed, the USS Sassacuswas, completely disabled and without propulsion, could only drift out of the Albemarle'a range with the currents.
The USS Miami joined the fray and tried to hook her spar torpedo mine into Albemarle but failed. Miami was receiving and firing shot from and into Albemarle while attempting to set a net in an attempt to tangle the Albemarle's propellers and rudder but this also failed. Miami then moved away from the battle and left the mighty Albemarle still in commission. In all, some 557 shells were fired by Union vessels at the Albemarle with the only visible damage being her smokestack and some of the iron plating. Nevertheless, the Albemarle was developing a mythical and fearsome reputation as the ship that would not sink. With darkness approaching, the Confederate legend steamed back up the Roanoke at Plymouth for needed repairs.
The repaired Albemarle now threatened the entire Union position on North Carolina's river system. Albemarle continued to successfully defend the region the approaches to Plymouth throughout the summer of 1864. The Federal Navy Department decided a special plan was needed to destroy the Albemarle and took on a plan submitted by Lieutenant William B. Cushing. The mission would require two small steam launches (otherwise known as a "steamer") that could be fitted with spar torpedoes. Cushing learned of a pair of such ships being constructed in New York and procured them for the attack. Each vessel was completed with a 14-foot spar to hold the torpedo as well as a Dahlgren 12-pounder howitzer for close-in, secondary defense. All told, the mission would be something akin to a modern-day, stealth-like commando raid.
Once finished, the two ships steamed away from New York towards Norfolk. However, one was lost at sea, forcing the remaining boat to take on the rescued crew. The personnel and vessel eventually reached Roanoke and prepared with its torpedo mine. From there, Lt Cushing made his way up the Roanoke river under the cover of darkness on October 27th with a small support cutter assisting. When they arrived at the site of the wreck of the USS Southfield they found a Confederate schooner anchored nearby. Without mush choice, the two vessels continued past the Confederate boat.
Despite their attempts at pure secrecy and stealth, the Union positions were finally discovered. Confederate forces opened up with small arms fire forcing the attacking vessels into decisions quickly. Cushing's vessel slipped over the slimed water logs protecting the Albemarle and brought the torpedo mine in close to the enemy ship. The torpedo was then detonated.
The resulting explosion killed a number of the men aboard the Albemarle. Cushing himself, as well as some crew, were thrown clear of their own vessel in the blast. The Albemarle was heavily damaged and left with a massive smoldering hole at the waterline to which she then sank in just six feet of water. Cushing and surviving members of his crew were able to swim to shore - some being captured. Cushing managed to hide under the overhung bank until daylight, avoiding enemy search parties throughout the night. The following morning, he found a small boat and used it to escape to the river's mouth, propelled in the water by his own hands. At least two fellow sailors died in the blast.
Albemarle now sat along the muddy river bottom with only her upper casemate above waterline. The Confederates ordered her surviving cannons to be used to defend Plymouth against the expected Union attack. The Union Navy now moved its river ironclads up the Roanoke and shelled the Confederate forts, ultimately capturing Plymouth.
After the end of the war, the Union gunboat USS Ceres towed the now-raised Albemarle to Norfolk, finally arriving there in April of 1865. She was repaired in August of that year but the Navy department decided to sell her at auction for scrap in October of 1867. Her only parts to have survived the war was a cannon and her smokestack, the latter on display today at the Museum of the Albemarle in Elizabeth City, North Carolina.
Lt. William Barker Cushing, USN, who planned and carried out the commando raid that sank the CSS Albemarle on October 27th, 1864, became a national hero to the North. Even Confederate Captain A.F. Warley of the CSS Albemarle said his exploit was a gallant thing. Admiral Farragut said young Cushing was the "hero of the war" and even President Abraham Lincoln added " I most cordially recommend that Lieutenant William B. Cushing, USN, receive a vote of thanks from Congress for his important, gallant and perilous achievement in destroying the rebel ironclad steamer Albemarle on the night of October 17th,1864, at Plymouth, NC. The destruction of so formidable a vessel, which had resisted the continued attacks of a number of our vessels on former occasions, is an important event touching our future naval and military operations, and would reflect honor on any officer, and redounds to the credit of this young officer....".