On December 7, 1798, Captain Barry was placed in "immediate command" of the frigates the "United States," the "Constitution," the "George Washington," the "Merrimac" with four or five more vessels of nearly the same force as the latter (24 guns). The fleet was to be employed in the West Indies in active operations for the "protection of our commerce and for the capture or destruction of French armed vessels from St. Christopher's as far as Barbadoes and Tobago," and to "pay considerable attention to Cayenne and Curricoa and even to the passage from the United States to Laguayra, on the Spanish Main, to which place our citizens carry on considerable trade," but above all, Barry was "to relieve our commerce from the piccaroons and pirates continually issuing from the Island of Guadeloupe."

Captain Truxtun was assigned "from St. Christopher's to Porto Rico," with two or three vessels of 14 and 18 guns. Captain Decatur, with one brig of 16 guns, "the vicinity of Havana," and Captain Tingley in the "Ganges," "between Cuba and Hispaniola," to give security to the trade of Jamaica.

The expedition was designed "to rid those seas as well of French armed vessels as of the pirates which infest them."

Barry was directed to "proceed as early as possible to Prince Rupert's Bay in the Island of Dominica, where the other vessels" of his command were ordered to rendezvous and he was to "commence operations." Under Barry's command on this expedition were Charles Stewart, Stephen Decatur, Jacob Jones, all of whom became famous in naval annals and obtained the highest positions. Barry's training and discipline developed heroes after his death. When the squadron reached the West Indies, Barry's command consisted of the frigate "United States," the "Constitution," Captain Samuel Nicholson; the "George Washington," Captain Patrick Fletcher; the "Merrimac," Captain Moses Brown; the "Portsmouth," Captain Daniel McNeill; the "Pickering," Master-Commandant Edward Preble; the "Eagle," Lieutenant Hugh George Campbell; the "Herald," Lieutenant Charles Russell; the "Scammel," Lieutenant J. Adams, and the "Diligence," Lieutenant J. Brown. The vessels sailing from Norfolk, Virginia, in company with Barry's frigate the "United States" were the "Constellation," of 36 guns; the "John Adams," the "Congress," the "Little Adams," the "Little York," all of 32 guns; the "Connecticut," the "Boston," the "General Green," of 36 guns; the "Siren" and "Argus," of 16 guns, and the "Enterprise," 14 guns. All ships "must claim your attention as well as your own," directed Secretary Stoddert.

The "Constellation" "cruised for about three months without finding any game," until she captured the "Insurgente," of 50 guns and 700 men of whom 350 were killed or wounded. The "Constellation" met a French, 74, later but the enemy being of superior force the "Constellation" "got out of reach." The next day the "United States" met the same French vessel and after an exchange of a few shots, Captain Barry also thought it advisable to withdraw, as his ship had become "dismasted" and had to go to Bermuda for repairs, while the "Constitution" was "much disabled in her mast and spars." Later Captain Nicholson captured the "Carteret," packet "and took her to St. Pierre" and again chased a French privateer into a harbor near that port.

On February 30, 1799, the "United States," under Barry, gave chase to a French privateer. A well-aimed 24-pound shot was sufficient to "cut the career of the privateer short," for the ball went through her hull so that she quickly began to fill and settle. Captain Barry ordered the boats of his frigate to the rescue of the crew. Midshipman Stephen Decatur being in the first boat to reach the wreck and rescue the crew. "They were plaintively imploring for help," wrote an eye-witness, "with earnest gesticulations, not only from men but from God and although it is 'true they had abolished all religion they had not, it seemed, forgot the old way of invoking the protection of the Omnipotent.'"

The vessel was the "Amour de la Patrie," of 6 guns and 80 men. All her crew were saved. The "United States" also captured the "Tartufe," of 8 guns and 60 men. Desiring to relieve himself of his prisoners and hoping to make exchange of Americans imprisoned at Guadeloupe, Captain Barry sailed to Basse Terre flying a flag of truce, but was fired on by the French batteries. Hauling down the flag Barry returned the fire and battered the walls so effectively that the marks of the American shot were visible for many years. The "Merrimac," Captain Moses Brown, captured "Le Bonapart le Phenix," 14 guns, 128 men, and "La Magiciene," 14 guns, 63 men. The "Portsmouth" took "La Bonapart" (No. 2), "Le Bullante," "Le Tripon" and "Le Bon Peré," of 6 guns and 52 men. Seven other captures made by the squadron.

It is not within the scope of this narration to record the operations of the fleet or the exertions of the several commanders of the respective vessels composing it, but much that was creditable to our naval forces was done though little that could be called brilliant or conspicuous, beyond the capture of the "Insurgente" by Truxtun and the "Amour de la Patrie" and "Tartufe" by Barry. The main service of the fleet was in protecting our merchant vessels and convoying them to safe waters.

Commodore Barry was not in good health while on this expedition. This, the Secretary of the Navy, writing to him, 15th March, 1799, chose to "attribute to vexation for not being able to fall in with the French" than to the effects of the climate. He had the "most entire confidence" that when joined by the other vessels Barry would "afford the greatest possible protection to our commerce and punish the depredation on it."

Barry had been joined by the "Constitution," the "Washington" and the "Merrimac" and would later have under his command the "Portsmouth," the "Herald," the "Pickering," the "Diligence," the "Scammel" and the "Eagle." Secretary Stoddert notified him, and also that if his health obliged him to return, Captain Truxtun would take command of the fleet and of the operations.