Aided by directions from some of the Native Americans along the Colombia River, the Lewis and Clark Expedition next reached the territory of the Walla Wallas. As they journeyed, despite the fact that most of the expedition's medicine had been lost in the incident with the nearly capsized boat, Clark became famous among the Native Americans for being a great medicine man and healer. Native people flocked continually to the expedition's campsite now, asking for help with everything from their sore backs to their eye problems. By the time the expedition reached the Walla Wallas, these people were greatly looking forward to receiving this now-famous healer.

Communication with the Walla Wallas proved a challenge, since the Lewis and Clark Expedition had no interpreter who could speak the Walla Walla language. The Walla Wallas, however, did have a Shoshoni prisoner who spoke Walla Walla and whom Sacajawea could talk to. So the complicated chain of communication went like this: Lewis and Clark spoke English to one of the expedition's English and French speakers, who translated the message into French for Charbonneau, who communicated the message to Sacajawea, who then relayed the message to the Shoshoni prisoner, who finally conveyed it to the Walla Walla chieftains. Thus once again Sacajawea proved to be a critical link in the success of the mission. By dealing with the Walla Walla through this complex communication chain, the expedition managed to greatly improve its supply of food. Spirits rose; it began to look like they might make it back east alive after all.

The expedition spent May and June of 1806 back in Nez Perce country. Unfortunately, the Shoshoni horses the expedition had left with the Nez Perce had largely scattered, and rounding them up took a long time. Meanwhile, Jean Baptiste ("Pomp"), who had amazingly endured rigors terrible for a grown man let alone an infant, finally came down with his first major sickness: a sore throat. Without medicine, which Charbonneau's incident in the boat had lost, the disease threatened the baby's life. Sacajawea and Clark tried all kinds of herbal remedies on the child however, and he miraculously recovered by the end of May.

On June 10, 1806, the expedition left the Nez Perce region. Now, they approached the Bitterroot mountains once again. Crossing for the second time, the group made it out of these mountains intact on June 29, 1806. Following this, Lewis and Clark decided to divide the party to do some quick exploring before heading home. Clark's group, which included Sacajawea and Charbonneau, would try to continue back the way they came, along the Yellowstone River, while Lewis's group would explore the Marias River. The plan was for both groups to meet in North Dakota.

Going upstream on the Columbia, against the current, the expedition moved slowly. This provided time for Lewis to get involved in some mischief. On the way to Walla Walla territory, Lewis convinced an uncooperative tribe to help the expedition by throwing an artillery fuse into the campfire--this caused an explosion and a tower of flame--and claiming to be a powerful sorcerer. The frightened Indians then were willing to offer help and trade with the expedition. Later, when Lewis's dog was stolen by another tribe along the way, he organized a group of the expedition's men to go on a rescue mission!

Meanwhile, Sacajawea's husband Charbonneau continued causing problems for the expedition, slowing them down. Charbonneau, inexperienced with horses, even lost two of the expedition's precious animals. Sacajawea, though burdened with Jean Baptiste, more than compensated for her husband's blundering ways. During the travels through Walla Walla and Nez Perce areas, Sacajawea was constantly gathering roots and other edible things, including fennel and yampa roots. Many of the sick men on the expedition started feeling better as Sacajawea helped add variety to their diets. Even Lewis, normally rather cold towards Sacajawea, noted in his journal that she had proven very helpful yet again.

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.