On July 25, 1781, Captain Barry reported to the Board of Admiralty that he was “almost recovered” of his wound and in a few days would be able for duty, his presence being very requisite on account of the scarcity of officers. He made recommendations for places. On June 24th Captain James Nicholson had written Captain Barry congratulating him upon his success. He related in detail the endeavors of Captain John Paul Jones by personal application to members of Congress to have himself declared “Head of the Navy.” He told Barry that his “arrival and success came opportunely and I did not fail to make use of it in presence of Captain Jones and some of his advocate members by observing that you had acquitted yourself well, which they acknowledged. I then told them they could not do less than make you an Admiral also. I had not a sentence in reply. It irritated Jones so much that he was obliged to decamp.” This shows that among naval men Barry was then regarded as “Head of the Navy” as he was in fact if not by title.

In 1781 the Admiralty and Navy Boards were abolished by Congress and all naval affairs given to the Finance Department, supervised by Robert Morris. At this time the “Alliance” and the “Deane,” frigates, constituted the whole of the effective navy. On September 21st Mr. Morris notified Captain Barry that it was projected to have the two frigates sent out upon a cruise under Barry’s command to “disturb the enemy” by taking prizes, and neither fixing the cruising ground nor its length of time, knowing Barry would take “the most likely course and be anxious to meet such events as will do honor to the American flag and promote the general interest.” He was to transmit at every opportunity reports of his operations to Morris and to General Washington any intelligence which may affect his operations. But, late in October, the “Deane” not being manned as soon as the “Alliance,” Barry was directed to proceed to sea as soon as the “Alliance” would be ready. But the victory at Yorktown on October 19th, when Cornwallis surrendered his army to the combined French and American forces and to the French fleet, caused a change to be made in the movements of the “Alliance.”

Instead of going out to seek prizes to procure funds to be applied to the support of the small navy, Captain Barry, on November 21, 1781, was directed to take Lafayette to France “on business of the utmost importance to America.” So urgent was this mission that Barry was directed to take part of the crew of the “Deane,” place them on the “Alliance” and to take such French seamen as the Consul could procure. If still short of men the Governor of Massachusetts should be applied to for permission to impress seamen wherever found. Besides Lafayette, his brother-in-law, Vicomte de Noailles, General Du Portail, Colonel Gouvion, Major La Combe and others were also taken on the “Alliance.”

Morris directed that “the safe and speedy arrival of Marquis Lafayette is of such importance that I think it most consistent with my duty to restrain you from cruising on the passage. You are, therefore, to avoid all vessels and keep in mind as your sole object to make a quiet and safe passage to some port in France.”

Regarding stores for the accommodation of the French gentlemen, “Let it be done with discretion; remember we are not rich enough to be extravagant nor so poor as to act meanly.” If funds were needed for a return cruise Barry was advised to “prevail with the Marquis to give you credit, but you must remember that all the money we have or can get in France will be wanted for other more important purpose, therefore, I charge you not to expend one livre more than is absolutely necessary.”

The “Alliance” sailed from Boston on December 23, 1781, and arrived at L’Orient, on January 18, 1782. During the voyage a British ship appeared in sight, “as if she could give them sport,” as Barry’s crew often wishing “Lafayette was in France,” stated it. Barry’s peremptory order to avoid all vessels and take no prizes debarred an encounter with the enemy. The crew manifested discontent at avoiding the possible prizes and, relates Kessler, this appeared to increase the conflict in Barry’s mind between the call of duty and his inclination. Instead of reprobating and promptly punishing what on other occasions would have been the case, he was governed by a sullen silence which, if propriety permitted him to break, would have pronounced: “I also wish the Marquis were in France.” But duty triumphed then as ever with Barry. As speedily as wind and wave and skill could force onward the “Alliance” she sped on her mission of the “utmost importance,” and in twenty-three days Lafayette was in France.

Barry’s instructions permitted him, after his placing Lafayette “in France,” to cruise in search of prizes until March 1st. The “Alliance” sailed from L’Orient on February 10, 1782, and returned after seventeen days without making any captures, the vessels met being neutral ships.

On March 16, 1782, the “Alliance” sailed from L’Orient for return to America and here again disappointment came. All the vessels spoken on the voyage “none were of the enemy.” On May 10th the “Alliance” arrived off the Delaware Bay. The British frigate “Chatham,” of 64 guns, and the “Speedwell,” sloop-of-war, barred entrance to the river, and off New York two more frigates joined in the chase of the “Alliance,” but she, having a speed of fifteen knots an hour, succeeded in escaping the much superior force and getting to New London, Connecticut, on May 13th. This incident was one of traditionary interest among the veterans of the old time wooden navy.

“Not a prize this trip! Hard luck indeed,” wrote Barry to John Brown, Secretary of the Board of Admiralty, to whom also he wrote that Robert Morris had sent him orders to join the French frigates at Rhode Island and be under their command. “Mr. Morris,” wrote Barry, “must be unacquainted with his rank or he must think me a droll kind of a fellow to be commanded by a midshipman. I assure you I don’t feel myself so low a commander as to brook such orders. I suppose he will be much offended. I assure you although I serve the country for nothing I am determined no midshipman shall command me, let him be a chevalier or what he will.”

Barry wrote from New London to Mr. Brown: “I never was in such a damn country in my life. You never was in so miserable a place in your life. All the people here live five miles from home. Not a house have I been in but the tavern and one Irishman’s.” The tavern was kept by Thomas Allen, an Irishman from the island of Antigua, whose “antipathy to the British was abnormal” and so we may well believe he was a kindred spirit to that of Commodore Barry.

Though Captain Barry thought he had “hard luck” in not taking a prize, yet the log-book of the “Alliance,” a copy of which he sent the Committee of Investigation, relates that on April 3d he fell in with two privateers, gave each of them a broadside, one of them struck, the other ran; hove out a signal for the “Marquis La Fayette” to take charge of the privateer that had struck while the “Alliance” went in chase of the other, “which we shortly after took.” The record again shows Captain Barry did as he usually had done captured two vessels in a battle.

Though he brought in no prize he yet was not unmindful of Mrs. Barry, but brought her a carpet and “a wash kettle full of claret,” and doubtless other luxuries of the time as well as advising her “not to stay so much at home,” as it “was clever to visit one’s friends now and then, besides it is helpful to good health,” added the gallant Captain.