Unlike the Native Americans of the Pacific Northwest, the Nez Perce wanted nothing to do with the blue beads that the expedition had run out of. Instead, they wanted practical items, and the expedition still had a few of these left. Thus trading proved much easier, and relations friendlier.

Sacajawea's presence with a baby continued to protect the expedition from Indian attack. On the way west, the Nez Perce had considered killing the expedition until they saw Sacajawea with her infant son. However, as Clark became increasingly famous as a healer in the area, it became less likely that any Native Americans would threaten the group, since they wanted medical help. The Nez Perce flocked to Clark to receive his healing, and he used the opportunity to give speeches about the United States and Thomas Jefferson, whom he called the "Great White Father." However, his statements to the Indians did not present the whole truth: he said that the United States wanted merely to establish trade, whereas of course the government had total appropriation in mind. Sacajawea had helped this expedition survive, and now its leaders began to pull the wool over the eyes of the Native Americans. Sacajawea directly participated in this too, since Lewis and Clark's speeches were communicated through her to a Shoshoni prisoner to the Nez Perce. (However, she may not have known the truth being concealed).

While Jean Baptiste's illness presented a problem for the expedition, it was quite amazing that the baby had survived so far. His survival must have largely been out of luck, but it also was a testament to Sacajawea's remarkably meticulous care that he remained alive while being carried outdoors for over a year from St. Louis to the Pacific, through the cold of winter.

The expedition's spirits fluctuated wildly during this period. When the group saw the Bitterroot Mountains, they erupted in happiness, believing they were almost home. However, crossing the mountains proved so difficult and the trail necessitated so much backtracking that everyone quickly became upset. Only the help of a Nez Perce guide got them across safely.

Splitting into two groups constituted a dangerous move, and each group feared it would never see the other again. Sacajawea went with Clark to help the group as they returned through Shoshoni country. As always, Sacajawea was a valuable guide, helping the group trace the Shoshoni trails through the region.

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