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Pleading illness, Richard Couthouy, the conchologist, left the expedition and departed for home. Added to the expedition through the recommendation of former President Andrew Jackson, Wilkes would have preferred another scientist and was suspicious of Couthouy from the outset. He soon proved to be an active promoter of discontent among his messmates, so much so that one of the enlisted men on Vincennes reported it to the commander while they were sailing between Samoa and Sydney. Wilkes summoned a meeting of the junior officers and confronted Couthouy directly. Wilkes called his conduct mutinous and threatened to maroon him on a desert island if he persisted. Couthouy stood discredited. Wilkes believed that the incident led to his request for detachment at Sydney, a request that the commander was pleased to grant. As events later transpired, Couthouy went only as far as Honolulu before deciding to try to rejoin the expedition, but Wilkes was determined that he had seen the last of the troublemaker and accused him of concocting the ploy to avoid work on the next leg of the expedition.


After enjoying Christmas Day in Sydney, the squadron departed on 26 December for Antarctic waters at the height of the summer season. They were stocked with ten months' provisions for their three-month voyage in case they became trapped in the ice and special care had been taken to make sure the ships were well caulked against leaks. Crewmen made hurricane shelters for themselves over their berthing for extra comfort from the weather and Wilkes performed inspections of the crew's uniforms twice a day in order to make sure they were dressed properly for the weather conditions.


The squadron enjoyed pleasant weather through 31 December, but on 1 January, at 48°S latitude, a heavy fog arose. Flying Fish fell behind and out of sight, so the other three ships headed for Macquarie Island, which had been designated as a rendezvous in event of separation. On 3 January, Vincennes and Porpoise lost sight of Peacock, but presumably all four ships were still headed for the pre-arranged meeting. Though they tried to make Macquarie Island on 7 January, Vincennes and Porpoise found that they had carried 20 miles too far in the night and Wilkes decided to by-pass the meeting altogether. As it happened, both Flying Fish and Peacock reached the island around 10 January, but Flying Fish anchored off the north side of the island and Peacock the south, so the ships did not meet. They waited the required 48 hours and then continued on their missions separately. Within a few days, Peacock caught up Vincennes and Porpoise, but the crews of these ships feared the worst for Flying Fish.


Vincennes and Porpoise first saw icebergs on 10 January at 61° 08' S latitude and 162°32' E longitude. They became more numerous and soon formed a barrier preventing passage further south. The ships followed the barrier to the west, looking for an opening. Because of Wilkes' desire to be the first to confirm the existence of an Antarctic continent and the punctiliousness that he practiced and demanded of his officers, some events of the next few days later became controversial. The published narrative of the expedition asserted that on 15 January Lieutenant Ringgold of Porpoise first claimed to see mountains in the distance. The next day all three ships reported that land was visible, and so Wilkes dated the discovery of Antarctica from that date. Eager to maximize the opportunity for gathering information, two days later Wilkes told the other ships that they no longer needed to remain in company and should rendezvous at the Bay of Islands, New Zealand in March. On the morning of 19 January he asserted land was most certainly visible.


The dates of these sightings became controversial after the completion of the expedition because of the manner in which they were recorded, or not recorded, in the ships' logbooks and the fact that a French expedition under Dumont D'Urville was also in the same waters and recorded discovery of land on the afternoon of the 19th. Who was first is still a point of dispute. On the afternoon of 19 January, D'Urville in his ship Astrolabe had sighted an explosed rock on an island, and in a style worthy of the great explorers of centuries before, landed on it with a French flag and claimed the continent for France, naming it Adelie in honor of his wife. They then sailed on, like the Exploring Expedition, seeking a way to it through the ice barrier. On 30 January at 135°E longitude, Astrolabe and Peacock sighted each other. After weeks of sailing in the desolate climate, the sight of another ship was a welcome one - at least at first. The two tried to come within hailing distance, but through a misinterpretation of each other's maneuvers both commanders came to the conclusion that the other wished to avoid contact. They sailed on, each convinced of the other's rudeness.


By the end of January, bitter cold and rain had sapped the health of officers and crew on all the ships. On the 24 January, Peacock almost met its end in calm, iceberg-laden waters. Too close to maneuver safely, first the bow, then the stern, hit large blocks. The rudder became useless. It was brought on board while the exhausted crew worked furiously to keep the ship from sliding into a nearby ice table whose walls were taller than their masts. During the night, which at that season was only about four hours long, its anchors did not hold and it crashed into the island, sustaining more serious damage, but none that affected its buoyancy. The crew worked the ship into open water by steering with its sails while the ship's carpenters made as good a repair as possible on the rudder. They then turned northward and returned to Sydney, arriving 22 February in serious need of an overhaul.


Porpoise and Vincennes continued exploring separately until 14 and 21 February, respectively. Vincennes pushed farther in spite of the crews diminishing health, including that of Wilkes himself. On 14 February crewmen went ashore on an ice island and were able to replenish their fresh water supply by cutting ice from a frozen pond. Turning north, Vincennes made for Sydney and arrived on 11 March. Porpoise arrived at the Bay of Islands on 26 March and waited for the others.


On arriving at Sydney, Wilkes heard of D'Urville's claim to discovering Antarctica. He immediately brought together all available log books from his ships in order to examine them for information to support of the Exploring Expedition's claim. At the time, he decided to report his discovery as being on the morning of 19 January, just hours before D'Urville's claim. It was only after the Expedition returned to the United States, that he clarified his position to cite 16 January. Still, he knew there would be controversy. In a generous act, and perhaps to underscore his primacy to a forthcoming British Antarctic expedition, he left its commander, Captain James Clark Ross, a note describing his findings with a map. On receiving the note, Ross would discount it.


Since 1 January, none of the squadron had seen or heard from Flying Fish. The crews of the other ships quickly became convinced that it had met the fate of Sea Gull. On arriving at the Bay of Islands, the crew of Porpoise was the first to discover, to their joy, that the ship had not perished. But it had faced the worst perils of all the ships.


After leaving Macquarie Island, the ship's commander, Lieutenant Pinkney, an officer whom Wilkes deemed incompetent, continued to sail south in accordance with his orders. The weather was foul and foggy, and this ship with the smallest complement soon felt its ill effects. It arrived at the Antarctic ice pack in late January and followed its edge, floating among bergs for more than a week in various kinds of weather while the members of the eight man crew became sicker and sicker. Eventually all enlisted and officers moved into the officers' small cabin, cooking on its tiny stove. Responding to the pleas of his crew, Pinkney turned the ship northward on 5 February and arrived at the Bay of Islands on 10 March. He set about repairing the ship, but when Wilkes arrived in New Zealand after making his stopover at Sydney, he found several reasons to berate the officer and finally replaced him with Lieutenant George T. Sinclair.