Orange Harbor, Tierra del Fuego and Cape Horn
Mindful of its shortcomings, Wilkes sent Relief onward to Orange Harbor, Tierra del Fuego after only three weeks in port. The rest of the flotilla waited at Rio de Janeiro for two more weeks while Peacock underwent extensive repairs. It had left Hampton Roads in less than ideal condition and now was in dire need of work to be able to survive the rest of the voyage.
While at Rio some of the scientifics took rooms ashore and pursued their studies. Horatio Hale, the ethnographer, was particularly interested in the physical characteristics of the African tribes represented among the slave population and Alfred Agate assisted his work. Wilkes established an observatory near the harbor's mouth for observations of weather and planetary magnetism, a practice that he would continue in ports for the rest of the voyage.
Finally on 9 January 1839 the rest of the ships set sail southward. In accordance with their orders, they stopped on the way to survey and investigate the commercial potential of the harbor at Rio Negro, but on 19 February they arrived at Orange Harbor, the first major stop for their exploratory endeavors. It was late summer in the cold climate. Commanders issued cold weather clothing to the crews after their departure from Rio, but it was found to be inadequate, a fault attributed to swindling government contractors.
Relief arrived on 29 January and began cutting firewood for the other ships. After a few days they began seeing native people, a sight that amazed them, because in the chilly climate they were almost naked, though for warmth on the water they burned small fires on heaps of stones and ashes in the wet bottoms of their canoes.
When Wilkes arrived at Orange Harbor, he believed that his instructions to Relief's commander, Lt. Andrew K. Long to prepare supplies for the other ships had not been followed properly. It reinforced his belief that Long lacked commitment to the purposes of the expedition. Careful preparations would be necessary for the survival of the ships in their various assigned tasks over the coming two months and all the crews spent the next four weeks preparing for it. Vincennes would remain at Orange Harbor and use its launches to survey Cape Horn. Relief would go into the Straits of Magellan to survey and describe the harbors there, along with most of the scientists, including Alfred Agate. The other four ships would go south. Wilkes in Porpoise with Sea Gull as its tender would head southeast towards Palmer's Land while Peacock, commanded by Lt. Hudson, with Flying Fish as its tender would go southwest to exceed, if possible, Captain James Cook's furthest voyage south - the "ne plus ultra" of 1774. On 22 February the squadron celebrated Washington's Birthday by flying their flags and issuing an extra ration of rum, a custom called "splicing the main brace," and on 25 February the ships separated on their various assignments.
Porpoise and Sea Gull had good weather for several days and then snow and foul weather set in as they explored the northern tip of Palmer's Land. The spent several days trying to proceed further south, but ice and bad weather turned them back on 5 March. Wilkes sent Sea Gull on an ultimately unsuccessful errand to Deception Island to look for a self-registering thermometer left in 1829 while he returned to Orange Harbor. Porpoise arrived there on Harbor 30 March.
Peacock and Flying Fish encountered squalls on their first day out and constantly throughout their voyage south. On the second day, the ships became separated. The expedition sustained its first fatality on 11 March when a sailor who fell from the maintopsail yard of Peacock into the sea two days earlier succumbed to his injuries. On the same day the Peacock sighted its first iceberg. By the 19th the ship was surrounded by them. On 25 March Flying Fish reappeared, and its commander, Lt. William Walker reported that they had been encircled by icebergs twice and finally stopped by them at 70° 14' latitiude, 105° W longitude, just short of Captain Cook's record. The commanders of the two ships consulted and reluctantly decided to head northward. Hudson took the battered Peacock to their next rendezvous point at Valpariso, Chile and sent word of his intentions with Walker to Orange Harbor.
Relief on its foray into the Straits of Magellan encountered harsh weather as soon as it left Orange Harbor. Wilkes claimed in his memoirs that he had instructed Lt. Long to hug the coast to be sheltered from the weather, but Long feared being driven onto rocks and headed for deep water. Whatever the case, storms soon forced him to seek shelter at Noir Island. There the crew spent a terror-filled night narrowly avoiding wrecking on the rocks. The ship lost its anchors in the fray and Long decided to discontinue his mission and head directly for Valpariso instead of returning, as ordered, to Orange Harbor. He attempted to send word to the Vincennes via a passing whaling ship, but his message failed to reach its destination.
After returning from his southward voyage Wilkes waited for two weeks for the return of the other ships. Flying Fish brought word of Peacock's whereabouts in the first week of April, but they had no information of Relief. Wilkes became worried, particularly for the well-being of the scientists on board. Still, there was no other reason to stay at Orange Harbor, so he left Sea Gull and Flying Fish to remain there for a few more days before joining him at Valpariso.
The two tenders waited until 28 April before deciding to move on. The fall season was far advanced and the inhospitable weather was worsening. The ships departed together, but encountered a storm on leaving Cape Horn. Flying Fish returned to the harbor for shelter, but Sea Gull sailed on. Flying Fish lost sight of Sea Gull near midnight. Sea Gull was never seen again and eventually it was presumed lost in the storm with its commander, Passed Midshipman James W. E. Reid, two other officers, and fifteen men.