The land that Troy occupies was once an old Sac and Fox campsite. The Sac and the Fox were independent tribes of the Algonquin who became allied as they were forced by the French to migrate south from the Great Lakes. A large band settled along the Missouri River and became known as the "Sac and Fox of the Missouri." European settlers began arriving in the area as early as the 1790s attracted by the Spanish land grants in the county's fertile Cuivre (French for copper) River Valley.
In 1801 Deacon Joseph Cottle erected a log cabin a short distance south of the public spring and Zadock Woods erected a double log house north of the spring. Cottle began operating a horse powered corn mill while Woods operated a tavern. In 1804 in St. Louis, Sac and Fox chiefs were persuaded to sign a treaty ceding to the U.S. Government all Sac and Fox lands east of the Mississippi River, as well as some to the west. Government efforts to enforce the land surrender raised tensions, particularly among the bands that were not party to and were unaware of the 1804 Treaty.
To defend their homes, pioneers in the area, aided by Captain Nathan (the youngest son of Daniel) Boone's Company of U.S. Mounted Rangers, built a series of forts (Woods, Howard, Stout, Clark, and Cap au Gris forts) as a first line of defense. Woods' Fort was built at the Cottle/Woods settlement and consisted of an almost square stockade made of strong oak timbers, set perpendicularly in the ground and extending to a height sufficient to afford protection from attack. Woods' Fort was the most extensive fort in the region and enclosed the spring, cabins, Woods Tavern and Inn, and Deacon Cottle's Universalist Church. Hostilities escalated when the War of 1812 began as the Sac and Fox sided with the British. During the war Woods' Fort served as headquarters for Lt. Zachary Taylor who later became the twelfth President of the United States. Hostilities ended when the Sac-Fox Treaty of 1815-1816 was signed.
The settlement that grew up around Woods' Fort became Troy when it was surveyed and laid out on September 19, 1819, by Deacon Cottle and others. The town was named by merchant Joshua N. Robbins after Troy, NY, which itself was named after the classical Troy, site of the Trojan War in Homer's "Iliad." Troy was selected in 1828 as county seat of Lincoln County, replacing Monroe and Alexandria. The town grew as a political and agricultural center using the river town of Cap Au Gris as a shipping point until the arrival of the St. Louis, Hannibal, & Keokuk Railroad in 1884. Lincoln County was sympathetic to the South during the Civil War but the almost continuous presence of Union troops in Troy kept the county free of any fighting.
At Fort Cap au Gris, Maj. (later U.S.Pres.) Zachary Taylor's command rendezvoused, Sept., 1814, and five months after the war, at Fort Howard, May 24, 1815, Black Hawk's band skirmished with settlers and Rangers in the Battle of Sink Hole. In 1824 the Sac and Fox finally gave up all claim to the region.