One of Fort Pike's less glamorous legacies came about due to the Seminole Wars, in which the United States fought to subdue, and ultimately relocate, the Seminole Indians from the new American state of Florida. These conflicts took place from around 1816 to 1858, and were an enormously expensive endeavor in both resources and lives. From the perspective of the nascent US government in the early 19th century, Native Americans were, by and large, an existential threat to the society that white folks hoped to build. In hindsight, it's easy to see why this opinion was formed, with Indians being generally less than receptive to being encroached upon by settlers, and with Great Britain frequently providing them with arms and encouragement to make things difficult for the United States...but Indians were also clearly considered to be less than human by the government, and a whole lot of unnecessary suffering and death resulted.

Fort Pike's part in all of this fun history is that it was a waypoint betwixt Florida and the western territories in which the government wished to place these Indians, so lots of Indians being prodded at bayonet point to their new homelands were stuffed into Fort Pike's casemates for brief periods during their trip. This casemate is adorned with two plaques memorializing this unpleasant period: In Respectful Memory and Honoring Seminole War Chief "Jumper".