When the USS Constitution was reaching the end of its fitting period, Nicholson received the authorization to recruit sailors and midshipmen, but the recruitment process was not met with much enthusiasm by potential recruits. This is due in part to Nicholson’s character, which often rubbed people the wrong way. A Boston Naval Agent described Nicholson as “a rough, blustering tar merely, a man whose noise and vanity is disgusting to the sailors”.
The USS Constitution was still not complete, and to speed up the process, sixteen 18-pound cannons were borrowed from Castle Island to be used on the USS Constitution. Finally, on the evening of July 22, 1798, the USS Constitution set out to sea. The USS Constitution was under the orders to patrol the Eastern Seaboard between New Hampshire and New York. In late May, President Adams ordered that all Navy ships patrol for French armed forces, and attempt to free American ships under French captivity. After a month of sailing between Chesapeake Bay and Savannah, Georgia, Nicholson capitalized on an opportunity to capture a prize off the coast of Charleston, South Carolina. On September 8, Nicholson and his crew intercepted Niger, a 24-gun ship commanded by a French crew claiming to be under orders from Great Britain. In spite of this, Nicholson captured the crew of the Niger, placed a prize crew (captured crew members put in charge of the captured ship’s operations) aboard Niger, and had her brought to Norfolk, Virginia. The USS Constitution sailed south a week later while escorting a merchant convoy, but a gale badly damaged her bowsprit and forced her to return to Boston. During this, Secretary of the Navy, Benjamin Stoddert concluded that the Niger was in fact operating under Great Britain, and the detained ship and crew were subsequently released. Because of this fiasco, the American Government was forced to pay a restitution fee of 11,000 to Great Britain.
The USS Constitution departed Boston on December 29 to report to Commodore John Barry (often referred to as “The father of the American navy”) off the island of Dominica to start patrolling the West Indies. By the fifteenth of January 1799, the USS Constitution intercepted Spencer, an English merchantman ship, that was captured a few days before by the French frigate L Insurgente. Perhaps unsure of himself after what happened with the Niger, Nicholson released the French ship and crew the following morning.
Extensive repairs on the USS Constitution for storm damage put the ship out of commission for awhile. However, n March 1, USS Constitution and HMS Santa Margarita agreed to a friendly sailing duel. After 11 hours, the Santa Margarita admitted defeat and payed the reward of a cask of wine to Nicholson. When USS Constitution resumed its patrol, she freed the American vessel Neutrality, and the French Carteret. However, Secretary Stoddert decided to recall USS Constitution to Boston where Nicholson would be relieved of his command.


