Later, en route to Hampton Roads to join the North Atlantic Blockading Squadron, the ship suffered mechanical difficulty and was detained at the Washington Navy Yard for repairs from 19 November 1863 to 22 January 1864.

On 1 February, Sassacus found the new and fast steamer, Wild Dayrell, near New Topsail Inlet, North Carolina, where the blockade runner had gone aground and discharged much of her cargo.

In March, Sassacus returned to Hampton Roads for repairs and then proceeded to the Washington Navy Yard to add two 12 pounder Dahlgren rifles to her battery.

On 26 April, Sassacus crossed the bar into North Carolina's inland waters and was assigned to Albemarle Sound, where other United States Navy ships awaited the reappearance of the dreaded Southern ram.

For about ten minutes, the ships were locked together and engulfed in steam, while Sassacus attempted to penetrate deeper into her adversary, and Albemarle struggled to pull free.

Sassacus, operating with only jury-rig repairs, remained in the sounds for over six weeks struggling to help maintain the Union's tenuous grasp on eastern North Carolina.

Then, steaming stern first to minimize the pressure on her battered bow, she headed for the James River, where Union strength afloat was needed by General Ulysses S. Grant in his drive toward Richmond, Virginia.

Early in November, Sassacus returned to Hampton Roads where preparations were underway for a joint Army-Navy expedition against Fort Fisher, which protected Wilmington, the Confederacy's last major blockade-running center.

During the ensuing weeks, the double-ender performed blockade duty off that strategic port and assisted the United States Coast Survey in the vicinity of the mouth of the Cape Fear River to obtain topographic intelligence for the forthcoming operations.

Army reluctance had been dispelled by Major General Benjamin F. Butler's fascination with a plan to destroy Fort Fisher by detonating an explosive-filled ship as close as possible to the fortress.

Sassacus, accompanied by Admiral David Dixon Porter's fleet, then got underway and towed the fully loaded Louisiana to the mouth of the Cape Fear, arriving off Fort Fisher on 18 December.

The task of leveling the Confederate works was left to naval gunfire, and Sassacus readily joined in the bombardment which began at daylight on Christmas Eve and was maintained throughout the day.

During the next two days, while laboring to return the last of the troops to ships, Sassacus's launch and second cutter were both damaged in the heavy surf, abandoned on the beach under orders from Brigadier General Newton Martin Curtis, and later destroyed.

Disappointed by Butler's indecisive leadership, Admiral Porter managed to get General Grant to commit the Army to a prompt return to Fort Fisher.

The new task force, containing a reinforced Army contingent commanded by Major General Alfred Terry, arrived at Beaufort on 8 January 1865 but was held up there by bad weather.

After the Confederacy collapsed, Sassacus cruised in the Chesapeake Bay to prevent any possible attempt of conspirators in the assassination of President Abraham Lincoln to escape by sea.