Upon Bainbridge’s return to Boston he attempted to regain command of the yard from his replacement, Captain Isaac Hull. Unsuccessful, he was instead appointed Port Captain (“commander afloat” of all naval vessels in Boston Harbor), with _Independence_ designated station flagship. Bainbridge settled down to a career as a senior officer, serving as commandant at the yard twice more in the 1820s and ’30s. He had helped put Charlestown on the map as the builder of a major warship. More significantly, after the War of 1812 the yard began building a reputation as an important repair and supply facility.
The Charlestown yard, and the U.S. Navy itself, owed their existence in part to the same Barbary pirates who occasioned _Independence’s_ first cruise. The severing of ties with Britain during the Revolution also meant the loss of protection from the Barbaries long provided by the Mother Country’s powerful navy and by the “tribute” Britain paid them. The United States had no navy to protect its seaborne commerce—so essential to a coastal nation dependent on overseas trade—and the treasury could not bear the tribute payments or the ransom demands for captured ships and sailors.
Thus after independence the Mediterranean trade had been virtually closed to the United States. There was much unresolved debate about the problem, but when the pirates spilled out into the Atlantic in 1793 and took 11 American vessels in a few months, Congress took action. The following year it authorized six frigates, three of which were launched in 1797: _United States_, _Constellation_, and _Constitution_.
Congress was spurred to finish the job by the actions of Revolutionary France during its war with Britain. French commerce raiders so terrorized American neutral shipping that in 1798 an angry U.S. government created the Navy Department and prepared for war. (There were a number of engagements at sea, but war was never declared.) Congress authorized funds to build, borrow, or accept as gifts 49 vessels, ranging from galleys to six 74-gun ships-of-the-line.
The 74s were never built, but while the program was still alive, naval shipyards to build them were established in Portsmouth, Boston, New York, Philadelphia, Washington, and Norfolk. Boston, wrote Secretary of the Navy Benjamin Stoddert to President John Adams, from “the natural strength of its situation [meaning its large, deep, and defensible harbor], the great number of ship carpenters in its vicinity, and of its seamen, must always remain a building place and place of rendezvous for our navy of the first importance.” Thus in 1800 the Charlestown Navy Yard was established.