On August 27th the expedition started afresh, with twenty-nine packhorses, heading across the mountains to other Indian encampments on another branch of the Columbia. Travel was slow, as in many places they had to cut a road for the ponies, and often the path was so rough that the heavily-burdened horses would slip and fall. Snow fell at one time, and added to the difficulty of the journey, but by September 6th they had passed the mountain range, and had come into a wide valley, at the head of a stream they called Clark's Fork of the Columbia. Here they met about four hundred Ootlashoot Indians, to whom they gave presents in exchange for fresh horses. Continuing again, they reached Traveler's Rest Creek, and here they stopped to hunt, as the Indians had told them that the country ahead held no game. After refurnishing their larder they pushed on westward, and ran into another snow-storm, which made riding more difficult than ever. Their provisions were soon exhausted, game was lacking, and the situation was discouraging. The march had proved very tiring, and there was no immediate prospect of reaching better country. Lewis, therefore, sent Clark with six hunters ahead, but this light scouting party was able to find very little game, and was nearly exhausted, when on September 20th Clark came upon a village of the Chopunish or Nez Percés Indians, in a beautiful valley. These Indians had fish, roots, and berries, which they gave the white men, who at once sent some back to Lewis and the others. These provisions reached the main party at a time when they had been without food for more than a day. Strengthened by the supplies, and encouraged by news of the Indian village, they hastened forward, and reached the Nez Percés' encampment.

Their stock of firearms and small articles enabled them to buy provisions from these Indians; and they moved on to the forks of the Snake River, where they camped for several days, to enable the party to regain its strength. They built five canoes in the Indian fashion, and launched them on the river, which they hoped would lead them to the ocean. Lewis hid his saddles and extra ammunition, and, having branded the horses, turned them over to three Indians, who agreed to take care of them until the party should return.

The Snake River, flowing through beautiful country, was filled with rapids, and they had many hardships in passing them. At one place a canoe struck a rock, and immediately filled with water and sank. Several of the men could not swim, and were rescued with difficulty. At the same time they had to guard their supplies carefully at night from wandering Indians, who, although they were friendly, could not resist the temptation to steal small articles of all sorts. The rapids passed, the river brought them into the main stream of the Lewis River, and this in turn led them to the junction of the Lewis and Columbia Rivers, which they reached on October 17th. Here they parted from the last of the Nez Percés Indians. The Columbia had as many rapids as the smaller river, and in addition they came to the Great Falls, where they had to lower the canoes by ropes made of elkskin. At one or two places they had to make portages, but as this involved a great deal of extra labor, they tried to keep to the stream wherever they could. At one place a tremendous rock jutted into the river, leaving a channel only forty-five yards wide through which the Columbia passed, its waters tossed into great whirlpools and wild currents. Lewis decided that it would be impossible to carry the boats over this high rock, and determined to rely on skillful steering of them through the narrow passage. He succeeded in doing this, although Indians whom he had met shortly before had told him that it was impossible. At several places they landed most of the men and all the valuable articles, and the two chief explorers took the canoes through the rapids themselves, not daring to trust the navigation to less experienced hands.

In this far-western country they were continually meeting wandering Indians, and they learned from them that the Pacific Ocean was not far distant. On October 28th Lewis found an Indian wearing a round hat and sailor's jacket, which had been brought up the river in trade, and soon after he found other red men wearing white men's clothes. On the thirty-first they came to more falls. Here they followed the example of their Indian friends, and carried the canoes and baggage across the slippery rocks to the foot of the rapids. The large canoes were brought down by slipping them along on poles, which were stretched from one rock to another. They had to stop constantly to make repairs to the boats, which had weathered all sorts of currents, and had been buffeted against innumerable rocks and tree-trunks. Then they discovered tide-water in the river, and pushed on eagerly to a place called Diamond Island. Here, Lewis wrote, "we met fifteen Indians ascending the river in two canoes; but the only information we could procure from them was that they had seen three vessels, which we presumed to be European, at the mouth of the Columbia."

They came to more and more Indian villages, generally belonging to the Skilloot tribe, who were very friendly, but who were too sharp at a bargain to please Captain Lewis. On November 7, 1805, they reached a point from which they could see the ocean. Lewis says: "The fog cleared off, and we enjoyed the delightful prospect of the ocean—that ocean, the object of all our labors, the reward of all our anxieties. This cheering view exhilarated the spirits of all the party, who were still more delighted on hearing the distant roar of the breakers, and went on with great cheerfulness."

It was late in the year, and the captain wished to push on so that he might winter on the coast, but a heavy storm forced them to land and seek refuge under a high cliff. The waves on the river were very high, and the wind was blowing a gale directly from the sea; great waves broke over the place where they camped, and they had to use the utmost care to save their canoes from being smashed by drifting logs. Here they had to stay for six days, in which time their clothes and food were drenched, and their supply of dried fish exhausted; but the men bore these trials lightly now that they were so near the Pacific Ocean. When the gale ended they explored the country for a good place to establish their winter quarters. The captain finally decided to locate on a point of high land above the river Neutel, well beyond the highest tide, and protected by a grove of lofty pines. Here they made their permanent camp, which was called Fort Clatsop. They built seven wooden huts in which to spend the winter. They lived chiefly on elk, to which they added fish and berries in the early spring. A whale stranded on the beach provided them with blubber, and they found salt on the shore. The winter passed without any unusual experiences, and gave the captain an opportunity to make a full record of the country through which he had passed, and of the Indian tribes he had met.

The original plan was to remain at Fort Clatsop until April, when Lewis expected to renew his stock of merchandise from the trading vessels, which visited the mouth of the Columbia every spring; but as the winter passed the constant rain brought sickness among the men, and game grew more and more scarce, so that it was decided to make an earlier return. Before they did this Lewis wrote out an account of his expedition, and arranged to have this delivered to the trading vessels when they should arrive, and in this way the news of his discoveries would not be lost in case anything should happen to his own party. The Indians agreed to deliver the packets, and one of the messages, carried by an American trader, finally reached Boston by way of China in February, 1807, some six months after Lewis himself had returned to the East. On March 24, 1806, they started back on their long route of four thousand one hundred and forty-four miles to St. Louis.

Searching for fish, they found the Multonah or Willamette River, and Lewis wrote that the valley of this stream would furnish the only desirable place of settlement west of the Rocky Mountains. Here he found rich prairies, plenty of fish and game, unusual plants of various sorts, and abundant timber. Soon they reached the village of the Walla Walla Indians, who received them so hospitably that the captain said of all the Indians they had met since leaving the United States this tribe was the most honest and sincere. With twenty-three horses, and Walla Walla Indians as guides, they followed a new road up the valley of the Lewis or Snake River, which saved them eighty miles of their westward route. It was still too early to cross the mountains, and they camped near the place where they had trusted their thirty-eight horses to their Indian friends the autumn before. The Indians returned the horses in exchange for merchandise, and Lewis provided them with food. In all these meetings the squaw wife of the French trader was invaluable. Usually Lewis spoke in English, which was translated by one of his men into French for the benefit of the trapper Chaboneau, who repeated it in the tongue of the Minnetarees to his wife; she would then repeat the words in the Shoshone tongue, and most of the Indians could then understand them, or some could repeat them to the others in their own dialect.

Early in June they tried to cross the mountains, but the snow was ten feet deep on a level, and they had to abandon the attempt until late in the month. They finally crossed, and found their trail of the previous September. At this point the party divided in order to explore different parts of the country. Lewis took a direct road to the Great Falls of the Missouri, where he wished to explore Maria's River. Clark went on to the head of the Jefferson River, where he was to find the canoes that they had hidden, and cross by the shortest route to the Yellowstone; and the two parties were to meet at the mouth of the Yellowstone River. Lack of game prevented Lewis getting far into the country along Maria's River. On this journey he fell in with a band of Minnetarees, and some of them tried to steal his guns and horses. The only real fight of the journey followed, in which two Indians were killed. He then continued eastward, and on August 7th reached the mouth of the Yellowstone, where he found a note telling him that Clark had camped a few miles below.

In the meantime Clark had explored a large part of the valleys of the Jefferson, Gallatin, and Madison Rivers, and had found a boiling-hot spring at the head of the Wisdom River, one of the first signs of the wonders of the Yellowstone. His journey was made safely and comfortably, although at one place he had to stop to build fresh canoes, and during this delay a band of Indians stole twenty-four of his packhorses.