The distinction of being the U.S. Navy's first flagship, where the "Flag of Freedom" was hoisted by John Paul Jones is held by what ship?

The U.S. Navy's first flagship, where the "Flag of Freedom" was hoisted by John Paul Jones, is the USS Alfred. This vessel played a crucial role in the early years of the U.S. Navy during the American Revolutionary War. As the first ship to carry the Continental Navy's flag, the USS Alfred symbolized the fight for independence and naval presence against British maritime power.

The ship was not just a flagship by name but also embodied the spirit and operational command of one of the most iconic naval figures in American history. John Paul Jones's leadership aboard the USS Alfred was a pivotal moment that contributed to the reputation and establishment of the U.S. Navy, setting the groundwork for future naval operations.

The other ships listed in the options have historical significance but do not hold the same distinction as the USS Alfred. USS Constitution, while famous, was launched later and is known for its combat victories and role in the War of 1812. USS Lion and USS Nautilus, while having their own historical contexts, do not relate directly to the flag hoisting event led by John Paul Jones. Thus, the choice of the USS Alfred is fundamentally tied to its status as the first flagship and the significant events that occurred under its command.