In 1809, another altercation with the Blackfeet resulted in Potts' death and Colter's capture. While going by canoe up the Jefferson River, Potts and Colter encountered several hundred Blackfeet who demanded they come ashore. Colter went ashore and was disarmed and stripped naked. When Potts refused to come ashore, he was shot and wounded. Potts then shot one of the Indian warriors and was instantly pierced with arrows so numerous, that, to use the language of Colter, "he was made a riddle of."^[11] His body was brought ashore and hacked to pieces. After a council, Colter was told to leave and encouraged to run. It soon became apparent that he was running for his life pursued by a group of Indians. A fast runner, after several miles the naked Colter was exhausted and bleeding from his nose but far ahead of most of the group with only one assailant still close to him.^[12] He then managed to overcome the lone man:

Again he turned his head, and saw the savage not twenty yards from him. Determined if possible to avoid the expected blow, he suddenly stopped, turned round, and spread out his arms. The Native American, surprised by the suddenness of the action, and perhaps at the bloody appearance of Colter, also attempted to stop; but exhausted with running, he fell whilst endeavouring to throw his spear, which stuck in the ground, and broke in his hand. Colter instantly snatched up the pointed part, with which he pinned him to the earth, and then continued his flight.— John Bradbury, 1817.^[13][14]

Colter took a blanket from the Indian he had killed. Continuing his run with a pack of Indians following, he reached the Madison River, five miles (8.0 km) from his start, and hiding inside a beaver lodge, escaped capture. Emerging at night he climbed and walked for eleven days to a trader's fort on the Little Big Horn.^[15]