The men of the Corps of Discovery had reason to hurry. They started construction on November 2, 1804, and finished the triangular fort by November 27. The winter that followed justified every day of labor. Temperatures plunged so severely that several expedition members suffered frostbite after only brief exposure to the elements. The fort provided shelter, but barely. This was not a permanent military installation; it was a survival camp, built from cottonwood timber by soldiers who knew that without walls between themselves and the Dakota winter, the expedition would end on the frozen banks of the Missouri. For five months, from early November until April 6, 1805, Fort Mandan was the farthest outpost of American ambition on the continent, a cluster of rough-hewn buildings where thirty-odd people waited for spring to carry them into the unknown.

President Thomas Jefferson had given Lewis and Clark more than an exploration mission. They were to establish the first official contact between the United States and the nations they encountered, to forge friendly relations, to prepare tribes for the arrival of American traders, and to assert United States sovereignty over land that Indigenous peoples had occupied for thousands of years. At Fort Mandan, these diplomatic goals ran into complicated reality. The Mandan were cautiously favorable toward an alliance, and when the expedition returned in 1806, they sent their chief Sheheke east to meet Jefferson in Washington, D.C. But the Mandan would not abandon their established trading partnership with Great Britain through Canadian traders. The Hidatsa were more direct in their resistance, often avoiding meetings with Lewis and Clark altogether. The five villages near the fort were not blank slates awaiting American overtures; they were sovereign communities with existing alliances, trade networks, and their own strategic calculations.

Lewis and Clark did not waste the winter. Not knowing whether they would survive the journey west, they spent the long frozen months compiling everything they had learned since leaving St. Louis. Descriptions of Missouri River tributaries. Observations about the Native nations they had encountered. Catalogues of plant and mineral specimens collected along the route. All of it went into a manuscript they called the Mandan Miscellany. Clark gathered information from chief Sheheke about the route westward, sketching preliminary maps of territory no European had documented. In the spring, the captains loaded the manuscript and specimens onto their large keelboat and sent it downriver to government officials in St. Louis. It was an insurance policy: if the Corps of Discovery vanished into the western wilderness, at least this record of their work would survive. From Fort Mandan onward, they would be traveling beyond the edge of every existing map.

The Corps of Discovery departed Fort Mandan on April 7, 1805, heading west toward the Rocky Mountains, the Columbia River, and the Pacific Ocean. When they returned in August 1806, they found only charred remains. The fort had burned to the ground, the cause unknown. Whether it was accident, lightning, or deliberate destruction by someone with reason to erase it, no record explains what happened. The loss was symbolic: the expedition had outgrown its winter shelter. But nature was not finished. In the two centuries since, the Missouri River has slowly eroded the eastern bank and shifted its course, carrying away the ground where Fort Mandan once stood. The original site is now believed to be underwater. A replica fort has been built near the estimated location, giving visitors a sense of the cramped, cold quarters where Lewis and Clark planned the most ambitious American journey of the nineteenth century.