In 1806, after the Lewis and Clark Expedition had ended, Sacajawea, Charbonneau, and their son Jean Baptiste went to St. Louis. The family considered living there, and Otter Woman, another of Charbonneau's wives, probably went along. Charbonneau could hardly stand to be in "civilization"-- although St. Louis was only a small town of a few streets--and he quickly left his family in St. Louis, going on a trapping trip back out in the wilderness.

Charbonneau did make some attempts to settle down. On October 30, 1810, Clark sold him some land on the Missouri River, and he and Sacajawea prepared to adjust to life as farmers. Within a year, however, Charbonneau had decided that farm life wasn't for him, and in 1811 sold the property back to Clark. Accompanied by Sacajawea, Charbonneau went back to the frontier to continue trapping and trading. Traveling up the Missouri, the couple came to Fort Manuel in South Dakota to trade. On December 20, 1812, Sacajawea was reported to have died of a fever at Fort Manuel. She would have been around 25 years old. In 1813, Fort Manuel was burned by Indians. Charbonneau lived on for years, dying in his 80s. Jean Baptiste, who went on to live a life of high adventure himself, died in 1866. Or at least, this is the "official" (white) story.

The Shoshoni claim that Sacajawea did not die at Fort Manuel. They say that she traveled to Shoshoni land to live with her tribe, dying only in 1884. In this version, even Jean Baptiste came to live with them, dying a year after his mother.

Clark raised Jean Baptiste with the help of several people he appointed to the job, and paid tuition to several clergymen to educate the boy. At age 16, Jean Baptiste joined the expedition of Prince Paul of Wurtemburg, a German prince fascinated by the American frontier. After serving as a guide for Prince Paul, Jean Baptiste returned with him to Europe. In 1829, Jean Baptiste came home to the United States, now fluent in German, Spanish, French and English. He remained one of the most capable and well-known guides for the Great Plains and Rockies for decades. The well-educated Jean Baptiste later traveled to California and became involved in mining for gold; some accounts hold that he died there in 1866, though of course this differs from the Shoshoni story.

Sacajawea's life after the Lewis and Clark expedition is quite poorly documented. What little is known is described above, although much of even this incomplete description is still debated. Indeed, these debates contribute to much of the interest in Sacajawea as a figure.

Most of the debate revolves around Sacajawea's death. The report from Fort Manuel describing a Shoshoni woman's death there does not specifically name Sacajawea, though it states that the woman was accompanied by a French interpreter (and indeed, the Shoshoni claim that the woman was not in fact Sacajawea). Due to an attack by the area's Native Americans, Fort Manuel was soon abandoned after Sacajawea's apparent death, and the commander took a little girl with him, whom many thought to be Sacajawea's child Lizette. The commander took the girl to St. Louis where it appears that Clark took custody of her, evidently feeling he owed a great debt to Sacajawea for all of her help. Lizette more or less disappeared from the records, however, and may have died young. Charbonneau had already left when Fort Manuel was attacked, and he clearly lived on for decades. While Sacajawea's later life was not well documented, Charbonneau shows up again and again in various records and lived until he was in his 80s, although he never did see his children again. A wide variety of people employed the trapper and interpreter, including a Prussian Prince who wanted to learn about Native American tribes. Charbonneau continued marrying young Indian girls throughout his life.

How much truth is there to the Shoshoni version of Sacajawea's life, most of which has come to us through oral history and legend? Several later scholars have tried to argue that the Shoshoni version is correct. Some of these scholars have been Native Americans themselves, and others have been novelists, seeking to make Sacajawea's story longer and more interesting. This story suggests that Sacajawea left Charbonneau after he continued acquiring more and more wives, all younger than Sacajawea. After leaving Charbonneau, the story says, Sacajawea went to live among the Comanche Indians, where she gave birth to more children, later returning to the Shoshoni. Those who argue for the Shoshoni story have some evidence: several visitors to the Shoshoni at this time speak of an Indian woman who spoke fluent French. None of these accounts mention Sacajawea directly, however, and these journal accounts provide only a tenuous basis for suggesting that Sacajawea lived on for so many years. There were many French-Canadian traders who might come into contact with the Shoshoni, and it is not inconceivable that some other Shoshhoni woman could have learned French. The story also claims a later reunion with both Charbonneau and Jean Baptiste. The reunion with long-lost family members near the end of her life seems too melodramatically perfect to be true. (Furthermore, it doesn't mesh with the better-documented lives of Jean Baptiste and Toussaint Charbonneau.) The Shoshonis' date for Sacajawea's death comes only from an old reverend's recollection that he buried a French-speaking Shoshoni woman that year. Thus although some people prefer the Shoshoni version of Sacajawea's post-Expedition years, and although this version certainly makes the better story, its claims seem unlikely.