[1] In September 1764, during his time as a privateer and merchant, Hopkins took command of the slave ship Sally, owned by Nicholas Brown and Company.

In late 1765, Sally arrived at its first trading destination in the West Indies, but the surviving African captives were in such poor health that most sold for very little.

Hopkins' disastrous command of Sally contributed to Moses Brown's turn against participation in the Atlantic slave trade.

On January 5, 1776, Congress gave Hopkins his orders:[6] "You are instructed with the utmost diligence to proceed with the said fleet to sea and if the winds and weather will possibly admit of it to proceed directly for Chesapeake Bay in Virginia and when nearly arrived there you will send forward a small swift sailing vessel to gain intelligence....If...you find that they are not greatly superior to your own you are immediately to enter the said bay, search out and attack, take or destroy all the naval force of our enemies that you may find there.

If you should be so fortunate as to execute this business successfully in Virginia you are then to proceed immediately to the southward and make yourself master of such forces as the enemy may have both in North and South Carolina...Notwithstanding these particular orders, which it is hoped you will be able to execute, if bad winds, or stormy weather, or any other unforeseen accident or disaster disenable you so to do, you are then to follow such courses as your best Judgment shall suggest to you as most useful to the American cause and to distress the Enemy by all means in your power.

Marines and sailors landed in "a bold stroke, worthy of an older and better trained service," capturing munitions desperately needed in the War of Independence.

[9] John Hancock, President of the Continental Congress, wrote Hopkins: "I beg leave to congratulate you on the success of your Expedition.

Your account of the spirit and bravery shown by the men affords them [Congress] the greatest satisfaction..." Not only did Hopkins' expedition get needed war supplies for the Continental Army, but it showed the British Navy that they would have to divert their ships from the belligerent colonies to protect non-belligerent areas, thereby leaving fewer British ships to fight on the war front.

The Continental Congress and individual state governors through their legislatures allowed privately owned ships to help in the battle against Britain by issuing letters of marque.

[12] Even with the impassioned defense of John Adams, the Continental Congress voted on 2 January 1778 to relieve Hopkins of his command permanently.

Substantiating this, John Paul Jones, who had been a lieutenant directly under Hopkins, gained great respect while continuing this same type of naval warfare against the much larger Royal Navy.

"[13] Hopkins's commission was terminated by the Congress on January 2, 1778, for a variety of reasons, perhaps including for his part in the arrest of Richard Marven and Samuel Shaw, a pair of early whistle-blowers, due to their having reported his torture of British prisoners of war.

[14] Hopkins's subsequent institution of criminal libel proceedings against Marven and Shaw is single-handedly responsible[unreliable source?]

[17] Hopkins adopted, and helped to popularize, the "Gadsden flag" that depicts a Timber rattlesnake with 13 rattles representing the 13 Colonies with the phrase "Don't Tread on Me" on a Yellow background.