Company C of the 13th Infantry arrived on June 15, 1866, with orders to build a fort using whatever they could find. What they found was adobe mud, cottonwood trees, and trouble. The second night, Sitting Bull himself led a Hunkpapa raiding party against the camp. For the next year, the garrison endured what amounted to a siege. Lakota warriors captured the sawmill and ice house, cut off access to the Missouri River, and forced the soldiers to dig wells near their quarters. The water from those shallow wells, contaminated by livestock, gave them dysentery. Captain William Rankin's wife spent that brutal winter alongside the troops, and back east, newspapers reported that the entire garrison had been massacred. The hoax spread from the Philadelphia Inquirer across the nation before Rankin himself wrote to the War Department to confirm he was very much alive.

In 1867, the Army purchased old Fort Union, a fur trading post two miles away that had been operating since 1829. They dismantled parts of it and hauled the aged timber to Fort Buford. The reason was practical: thirty years of seasoning had made the wood far superior to the green cottonwood available along the rivers. By 1871, Colonel William Hazen's 6th Infantry arrived with lumber shipped by steamboat from the eastern states, expanding the post to nearly a square mile. A stone powder magazine built in 1875 from locally quarried sandstone held over a million rounds of ammunition. After the Battle of Little Bighorn in 1876, the fort became a critical supply hub for the Montana campaigns, swelling to nearly 100 buildings and 1,000 people.

Around 1870, an unexpected community formed two miles northwest of the fort. Some 150 to 200 Hidatsa and Mandan people, led by chiefs Bobtail Bull and Crow Flies High, had fled the Fort Berthold Reservation nearly 100 miles downstream. They built log cabins and sought protection from the very soldiers fighting their Lakota neighbors. The Hidatsa had never taken up arms against the U.S. Army, and proximity to the military offered safety. They served as scouts and mail carriers, traveling to distant outposts like Poplar and Glendive in Montana. The arrangement lasted until 1884, when the commanding officer closed the settlement citing overcrowding and various moral concerns.

Fort Buford was never meant to last. The original adobe and cottonwood buildings began collapsing almost as soon as they were built. The 1889 attempt to install water mains failed because workers could not bury pipes deeper than eight feet, not nearly enough to prevent freezing in North Dakota winters. When the Army decommissioned the fort on October 1, 1895, most structures were auctioned off and hauled away. Only three survived: the 1872 Commanding Officer's Quarters where Sitting Bull surrendered his rifle, the stone powder magazine, and a duplex that burned in 1937. The Mercer family used the headquarters as a granary and called the grounds Villa Militare until donating them to North Dakota in 1927.

Today the North Dakota State Historical Society maintains Fort Buford as a state historic site, though only 40 acres of the original square mile remain in public hands. A reconstructed adobe barracks built in 2004 shows what Company G's quarters looked like in 1876, based on archaeological excavations that revealed their daily lives. In the cemetery, a weathered marker tells the story of an Indian scout named He That Kills His Enemies, who died on January 18, 1870, from an arrow wound received in a quarrel with a fellow scout. No autopsy was performed, the stone notes, owing to the feelings of relatives. Such details humanize this remote place where empires clashed and cultures collided at the meeting of two great rivers.