West Coast of North America
On leaving the Kingsmill Group, Hudson had to put his crews on reduced rations because they were running low on supplies. After surveying a few more islands in what is now called the Marshall Islands, he decided that time was too short to continue and turned the ships toward the Columbia River, stopping at Honolulu to replenish supplies. They only stayed a week and continued to the northwest coast, arriving 16 July, a month and half late for their rendezvous.
When he arrived at the mouth of Columbia, Hudson had with him the instructions for navigating the bar that Wilkes had obtained from the master of a merchant ship he had met at Honolulu. As that ship had just come from the Columbia, he had no reason to doubt his instructions and he was not surprised to find treacherous conditions. These waters had a reputation for shipwrecks. While Wilkes had given up trying to cross when he arrived in boisterous weather, Hudson arrived in clear weather and had as good conditions as a captain of that era might expect in the unimproved channel. He also knew that his arrival was very late and he had experienced Wilkes' wrath when he tried to second-guess the commander's specific instructions on other occasions. On the 18th, following the Sunday morning service, he tried to guide Peacock through the bar.
After breaking off his first attempt to enter, Hudson steered the ship towards a portion of the water that appeared clear and smooth. The water was too shallow and the keel hit bottom and stuck. The current and tides then began to force the ship onto a shoal. Hudson ordered the sails taken in and prepared to drag the ship off by kedging - towing the ship's anchors out a distance and then pulling the ship towards them by winding the chains on the capstan. The weather in the sound defeated him before he could complete the plan. The sea began to lift and drop the ship, causing leaks. The crew manned the pumps. They fought to save the ship all day and night, and at dawn the tide receded so much that a canoe manned by Chinook Indians and carrying a pilot was able to come on board. Peacock launched it boats and filled them with as much as they could of the ships charts, books and papers. The boats made two trips between ship and shore, but eventually the scientific specimens on board had to be abandoned. Because of their survival, Alfred Agate presumably carried off some of his sketches. The surging currents rose again towards noon and overwhelmed the ship. Captain Hudson and some of crew remained on board during the evacuation, trying to save as much as they could, even by throwing light items overboard to be carried ashore by the tide. Finally at 5 pm Hudson was the last to leave the ship. By the next day Peacock had broken into pieces.
No lives had been lost in the wreck of Peacock, but some men had sustained significant injuries, including broken bones, and now they had no quarters. On shore, some people of the Methodist mission at Astoria brought them tents and supplies to make them comfortable. The sailors dubbed their little tent city "Peacockville."
In spite of the loss, the injuries sustained, and the hardship suffered by the shipless crew, everyone still pressed on with their assignments. The scientifics went into the field immediately and began making collections. Alfred Agate made some drawings of the local Chinook Indians and the tomb of Concomely (Concomly), a Chinook chief who had welcomed the explorers Lewis and Clark (who spelled his name Com-com-moly) and helped settlers build Astoria. Wilkes gave up his idea of exploring inland as far as the Yellowstone River and decided to concentrate on the little-known area of southern Oregon and northern California. He made up an exploratory group from the crew of Peacock and included the scientifics Peale, Rich, and Agate, as well as a few local trappers, and placed them under the command of Lieutenant Emmons. Their mission was to march south, surveying and describing the land as much as possible and join up with boats from the expedition at the most inland point of navigation of the Sacramento River. The rest of the expedition would meanwhile complete their own surveys and travel around by water to meet them.
To replace Peacock in the survey work, Wilkes purchased the brig Thomas Perkins from the Hudson Bay Company and renamed it Oregon. Wilkes gave Hudson the task of outfitting it, but when it was ready, Hudson suggested that command be given to another. He may have done this after sensing Wilkes' displeasure, but also, command of a ship as small as a brig usually went to an officer of lower rank and experience than he. Wilkes was only too happy to oblige Hudson and gave command of Oregon to Lieutenant Overton Carr, who had been serving as his executive officer on Vincennes. He then sent Oregon off to survey the coastline and Hudson became a supernumerary officer on Vincennes.
Lieutenant Emmons' party started south through Oregon along the banks of the Willamette River. They had hardly begun when they were forced to camp for almost five weeks as almost every member of the party, including the scientifics, became ill with "ague and fever." Ague in modern terms is seen as a catchall reference for a wide range of conditions, including malaria, but in medical terms of the day it meant a fever with chills. It delayed them until the first week in September. By that time Lieutenant Johnson's party had arrived from the east and Wilkes sent the scientifics Dana and Brackenridge to join Emmons, along with Midshipment Eld and Colvocoressis to carry out meterological observations.
When they finally returned to the trail they made good time, though repeated bouts of ague and their inexperience in wilderness ways caused them a few delays. Considerable time was spent on any number of mornings recapturing their horses. From the back of his horse, Agate drew constantly. They passed through the lands of various Indian tribes, the Callapuya of the Willamette Valley, the Umpqua of the Elk Mountains, and the Shasta and the Klamet (Klamath) of southern Oregon, the Sacramento of northern California. The Oregon tribes had reputations for being particularly hostile to whites; the agent at Fort Umpqua told the party that word had spread through the region of their approach and bands had collected to annihilate them. In the end, however, Wilkes noted that his men and other whites met with little hostility and postulated that the native peoples desired the trade that they brought.
Throughout the journey, the scientifics made new discoveries. One of the most significant botanical collections of the expedition was made by William Brackenridge on this part of the journey, near Mount Shasta: Darlingtonia californica, or the cobra lily. On 30 September they reached the ridge of the boundary mountains between Oregon and Mexico and saw Mount Shasta in the distance.
On emerging from the mountains they encountered Shaste (Shasta) Indians, who were friendly and eager for trade. When Alfred Agate tried to draw portraits of them, they believed him to be a medicine man trying to place a charm on them. The party soon reached the head of the Dangerous River, which fed into the Sacramento River, which they followed south to their rendezvous point, going east of it when the terrain was easier. They arrived at John Sutter's "New Helvetia" settlement on 19 October. At this time it was a thriving agricultural settlement, a few years before of the discovery of gold that would change its history forever. A few years later, surveying data gathered by the party would be useful to prospectors making their way to the California central valley. At New Helvetia, the party split. A launch from Vincennes took the sickest, including Lieutenant Emmons and Alfred Agate, from a nearby point on the Sacramento River to the ship in San Francisco Bay, making the journey in five days. The rest of the party continued on foot under Midshipman Eld's leadership and arrived at Yerba Buena (the early name for the city of San Francisco) on 28 October. They had not shaved in many days and were dirty and clad in buckskins, giving everyone the impression that they were a party of trappers. Eld recorded how one man there persisted in speaking Spanish to him, refusing to believe he was an American. Their faithful horses were sold at a public auction - a painful scene to the travelers - and then the explorers re-embarked on their ships.