Possibly the highlight of her medical service began on March 8, 1862 when she received on board men who had been wounded during the deadly foray into Hampton Roads of CSS Virginia, the former Federal screw frigate Merrimack which Union officers had put to the torch and scuttled just before abandoning the Norfolk Navy Yard almost a year before.

Raised, rebuilt, protected by a thick covering of iron plates, and armed with a sharp, strong prow, the Southern ironclad ram had proved to be almost impervious to shot and shell as she destroyed Union frigates Congress and Cumberland and damaged other Federal warships before withdrawing for the night.

Built with a flat deck and an extremely low freeboard, Monitor's hull above the waterline was protected by strong iron plate which, the following day, enabled her to fight her Southern ironclad opponent to a standstill.

Meanwhile, the buildup of the fleet to tighten the Union blockade of the South increased the Navy’s need for arms and ammunition in Hampton Roads, and the task of storing ordnance supplies was added to Ben Morgan's duties.

In June 1862, when the Navy occupied a vacant building near Fort Norfolk, Ben Morgan's embarked medical team — headed by Assistant Surgeon James H. Macomber — went ashore to turn that structure into a temporary naval hospital.

Early in the spring of 1863, the ship was surveyed and condemned; but the need for her services had proved so great that she continued to function in Hampton Roads until autumn when she entered the Norfolk Navy Yard for repairs and recaulking.