Continuing what I have been reading from the actual historical documents themselves. This is not the only point of view. I will put at the bottom my sources that I am using for this part.
Lt. Col. Duncan Clinch with his regiment of the 4th Infantry built Keel boats and descended down the Chattahoochee River from Fort Gaines to where they established Camp Crawford, later renamed Fort Scott, at the confluence of the Flint and Chattahoochee River. The abandoned Nicholls Fort or Fort Apalachicola was only a short distance down the river, on the Apalachicola River, at what is today Chattahoochee Landing on top of a large Indian Mound.
Below: Keel Boats on the Ohio River, 19th Century. They were made out of whatever was on hand, and the river work horse of the day. Usually once down river, would be sold or salvaged.
Supplies for the new American fort had been ordered from New Orleans, escorted by two gun boats, Gun Boat 149 and Gun Boat 154. The boats were waiting down in Apalachicola Bay. On July 15th, (1816) Lt. Col. Clinch received a message from an Indian named Lafarka, later known as John Blount that Sailing Master Loomis was ready to proceed. If they passed by the fort and were challenged, and they most assuredly expected they would, then they would destroy it. Clinch would attack Negro Fort from land, and the ships would fire from the river. Clinch departed Camp Crawford on July 17th with 116 men in the boats, and were soon joined by 150 Creek warriors under William McIntosh, and later still more warriors under Captain Isaacs and Mad Tiger, but many without armaments.
Below: "John", sketched by artist John Trumbull during Creek Chief's visit to President George Washington in 1790. Some have guessed that this might be Lafarka/Chief John Blount/Blunt, but it is only speculation.
The Creek allies had left on their own expedition to attack the fort and secure the slaves. McIntosh says that he intended to return them to their masters, but seeing how he was also in business with the Creek Agent David Mitchell, as would be revealed later, of illegally smuggling African slaves into the United States, he probably had intended to seize them for himself for sell. Soldier Marcus C. Buck says that many slaves from the United States and friendly settlements of Indians near the Apalachicola were apprehended on the way down.
Clinch’s report identifies the fort as being occupied by “Negroes and Choctaw Indians.” 80 to 100 Black Warriors, trained by the British, 25 or 30 Choctaw warriors, and the rest of the two-thirds being women and children. On the 19th, the Creek allies bring in a captured black warrior, carrying the scalp of one of the sailors, Midshipman Lufborough, saying they had killed several white men and captured their boat. (More of that later.) And they were taking the scalp to the Seminoles. Meanwhile, Lafarka reported that he was unable to get through and send another message to the ship captain down in the bay.
Clinch writes that he found 50 miles of corn fields cultivated along the river. We would assume that this would be for a population much greater than the 300 that were found inside the fort when the Army and Navy command reached it. Clinch was also of the belief that the fort only had six artillery pieces and that he could easily take it, which he soon found to be seriously mistaken.
Below: From Florida Memory: Sketch of Fort Gadsden(1818) with earlier British outer walls and circular protected British magazine:
Clinch landed his command on July 20th three-quarters of a mile from the fort. The fort was heavily armed with ten artillery pieces that kept up a constant fire of round shot, grape shot, and rockets. Although, the soldiers kept far enough back so it had no effect. Both sides remained harassing each other for the next week without any effect. Clinch tried unsuccessfully to set up a cannon battery on the opposite bank of the river from the fort. Clinch’s command will end up being mostly useless except surrounding the fort and keeping the occupants inside. Clinch's force is too small to lay siege to a well protected fort, and anyone in the fort is not able to wander outside very far without running into Clinch and McIntosh’s line. A classic standoff, and Clinch doesn’t have the supplies to sustain it for very long. The fort has enough supplies to wait out almost indefinitely.
Below: Photo from Florida Memory website. Cannon shot and Grape Shot excavated at Fort Gadsden/Negro Fort.
A deputation of Creek chiefs entered the fort but were much taunted and abused by the black chief and Choctaw chief inside, who said that they would attack any American vessel that tried to pass.
On the 26th, Clinch sneaked past the enemy lines to rendezvous with Sailing Master Loomis four miles below the fort at Dueling Bluff.
Next part gets really interesting, as I detail the battle of Bloody Bluff and the ambush upon the five sailors, where I go into the Naval accounts.
Taken from: The Army & Navy Chronicle, Vol. 2, No. 8, Page 114-116, Feb. 25, 1836
Navy Doc. # 119, Letter from the Secretary of the Navy, Transmitting, in Obedience to a Resolution of the House of Representatives, of the 26th Ult, sundry Documents relating to the Destruction of the Negro Fort in East Florida, in the Month of July, 1816. February 1, 1819. Washington, 1819.