On June 10, 1806, the Corps of Discovery left Camp Chopunnish on the Clearwater River and moved up to higher ground on Weippe Prairie. They had waited over a month for the snow to melt in the Bitterroot Mountains so that they could proceed eastward on the Lolo Trail. They set out on the trail on June 15, but soon realized that they could not find their way in the deep snow. On June 17, after caching many of their goods in trees, they turned back. Lewis lamented, "this is the first time since we have been on this long tour that we have ever been compelled to retreat or make a retrograde march." To add discomfort to discouragement he also reported, "it rained on us most of this evening."
They returned to Weippe Prairie and sent to the Nez Perce camps to hire guides. Three young men offered to serve for the price of two guns. On June 24 the party set out again. The Indians found the trail easily and the party made their way to their old camp at Travelers' Rest, near present Missoula, Montana, taking only six days in contrast to the eleven days of the westbound trip. They spent a few days resting for the next stage of the journey. At Fort Clatsop the captains had decided to divide the party for an extended time to investigate previously unexplored territory. Lewis would head east across the mountains to the Great Falls of the Missouri, then explore the Marias River before returning to the Missouri. His purpose was to discover if the Marias drained northern reaches thus giving further territorial claims to the United States under the Louisiana Purchase. Clark would go southeast to the site of Camp Fortunate, then down the Beaverhead and Jefferson rivers to the Three Forks of the Missouri. Part of his party would then take canoes down the Missouri to the Great Falls to meet Lewis's party there, while Clark went east to the Yellowstone and down that river. His object was to inspect the Yellowstone and perhaps make contact with additional Indian tribes. The two captains and their men would meet at the mouth of the Yellowstone.
On July 3 the two groups went their separate ways, Lewis admitting "I could not avoid feeling much concern on this occasion although I hoped this separation was only momentary." It was the first time during the expedition that they had separated for so great a distance and time. Lewis headed down the Bitterroot River, then up the Clark Fork and across the Continental Divide along a route suggested by the Shoshones and other Indians. By July 13 he and his nine men were at the Upper Portage Camp above the Great Falls, delighted after months of poor rations to be back in buffalo country. When Lewis's men dug up the cache at the camp they encountered problems with the host of grizzly bears in the vicinity. Hugh McNeal had a very close call with one beast in which he broke his musket over its head.
Several of their horses disappeared, probably stolen by Indians, so Lewis decided to take only his three best men—George Drouillard and Reubin and Joseph Field—on his exploration of the Marias. Sergeant Patrick Gass and the others remained at the Great Falls to await the canoe party from the Three Forks. Lewis and his companions set out on horseback on July 14, heading north to the Marias and then upriver to the stream's upper forks. On Cut Bank Creek, near the mountains, they camped from July 20 to 26, waiting for the clouds to clear so Lewis could take astronomical observations; Lewis was disappointed to discover the Marias did not extend so far north as he had hoped. On July 26 he gave up and set off for the mouth of the Marias, leaving what he named Camp Disappointment.
That afternoon they met eight Indians who proved to be Piegan Blackfeet, a tribe Lewis and his small party had wanted to avoid. They talked and all agreed to camp together that night on Two Medicine River. Lewis was awakened the next morning by sounds of a struggle as the Indians tried to make off with the expedition's guns and horses. Reubin Field stabbed one of the Indians to the heart, then the party pursued the others who were fleeing with the horses. Lewis was forced to shoot one of the Blackfeet in self-defense. It was the first and only instance of actual armed violence between the explorers and Indians in the whole expedition.
Lewis, Drouillard, and the Fields fled southeasterly as fast as they could. On July 28, near the mouth of the Marias River, they met the six men from the Great Falls, along with Sergeant John Ordway and nine others whom Clark had sent down from the Three Forks. They moved quickly on to the mouth of the Marias and retrieved cached goods and the white pirogue there. Then Lewis and his united group were able to travel down the Missouri with relative ease and speed.
At the mouth of the Yellowstone, which they reached on August 7, the remains of a note indicated that Clark had gone on down the Missouri. Lewis followed, taking time to hunt for food. On August 11 he was hunting on the banks of the river with Pierre Cruzatte when the Frenchman, thinking the captain was an elk, accidentally shot him in the thigh. The journey continued with Lewis in considerable pain, and on August 12, below the Little Knife River in North Dakota, the two captains and their parties were reunited.
Clark's party had had their difficulties, but their trip had been idyllic compared with Lewis's. Like Lewis, Clark had left Travelers' Rest on July 3, moving southeast over some new terrain across the mountains to their old Camp Fortunate at the forks of the Beaverhead River. There the party recovered cached goods and canoes and traveled down to the Three Forks by both canoe and horseback, arriving on July 13. From the forks Clark dispatched Ordway with the canoes down the Missouri to the Great Falls. Clark himself with twelve persons, including Charbonneau, Sacagawea, and their child, headed for the Yellowstone, which they reached on July 15.
They continued down the Yellowstone on horseback, but on July 18 George Gibson was injured and could not ride after his horse threw him, so Clark decided to make canoes and continue by water. On the twenty-fourth he set out again, sending Sergeant Nathaniel Pryor with three men and the horses to travel overland to the Mandan villages. Pryor was to make contact with trader Hugh Heney, going north into Canada if necessary, to secure Heney's services as an intermediary with the Sioux. Pryor's mission ended prematurely on the second night out when Indians, probably Crows, stole his party's horses. He and his men made Mandan-style "bull boats" of buffalo hides and floated down the Yellowstone and the Missouri pursuing Clark, whom they overtook on August 8.
Clark's trip down the Yellowstone was uneventful. He passed the landmark he named "Pompy's Tower"—after little Jean Baptiste Charbonneau—on July 25, near present Billings, Montana, and proceeded on, arriving at the mouth of the river on August 3. The original plan was for him to wait there for Lewis, but the mosquitoes were terrible and game was scarce so he left a note for Lewis and continued down the Missouri. On August 11 Clark's party met two trappers, Joseph Dickson and Forrest Hancock, the first whites they had seen since April 1805. These men could provide little information from the East, since they had been absent since the summer of 1804. They did, however, inform Clark that the Missouri River tribes were fighting one another again. The captain realized that his and Lewis's successes at peacemaking had been limited and of short duration. The next day the wounded Lewis and his contingent caught up with Clark.
The discomfort of his wound now caused Lewis to give up his journalizing, leaving Clark to continue the record to the end of the trip. Characteristically, Lewis's last entry included the description of one last plant, the pin cherry. The Corps returned to the Mandan villages on August 14. They remained there only three days, trying to persuade Mandan and Hidatsa chiefs to go with them to see the president, but only Sheheke, the Mandan, and his family consented. Charbonneau, Sacagawea, and Jean Baptiste remained behind, and John Colter received a discharge so he could return to the mountains on a trapping venture with Dickson and Hancock.
As they headed downriver on August 17 their thoughts were all directed toward home. They stopped overnight on the twenty-first at the Arikara villages, where they found the Indians unhappy because a chief sent to Washington the previous year had not returned. No other chiefs would agree to go. On August 30 they gave some Teton Sioux the cold shoulder because of the troubles they had had with this tribe in 1804. They met with the Yankton Sioux near the mouth of the Niobrara on September 1, and held a friendly council. On September 4 they revisited Sergeant Charles Floyd's grave near the mouth of the Big Sioux River.
They were now meeting trading parties bound upriver, who gave them the news of over two years, including the fact that most people in the United States had given them up for lost, although "the President of the U. States had yet hopes of us." Lewis was recovering from his wound as they daily passed camp-sites and other familiar scenes of the toilsome upriver trip. In the last days of the journey the men were troubled by sore eyes, but they pushed on, eager to reach St. Louis. On September 20, near La Charette, they saw cows for the first time since leaving the settlements. Soon the inhabitants of the little settlement greeted them enthusiastically. The next day they reached St. Charles, meeting old friends, and on the twenty-second they saw a significant omen of change, the first American fort west of the Mississippi at Belle Fontaine a few miles above the mouth of the Missouri.
Emerging from the river's mouth on September 23, they briefly visited the camp at Wood River that they had left some twenty-eight months before, then sailed on and reached St. Louis at noon. The citizens, having received advance word, lined the riverfront and cheered. Two days later, at Christy's Tavern, they were treated to a lavish dinner, with eighteen toasts, ending with "Captains Lewis and Clark—Their perilous services endear them to every American heart." The next day Clark brought his journals to an end with a brief, anticlimactic entry: "a fine morning we commenced wrighting &c."