Peacock arrived on 1 May and the scientists assigned to it, including Agate, returned to their assigned berthing. Three days later the squadron left for the Fiji Islands. On arriving at Ovalu Island they were met by David Whippy, a Nantucket sailor who had settled there. Whippy proved himself useful, acting as interpreter and advisor on local customs. An important piece of advice he offered was to never completely trust the Fijians. Both Whippy and the local missionaries told stories of treachery and murder among the island's cannibal population. In response, Wilkes issued orders for extra care when in contact with the islanders. Landing parties could only leave the ships when absolutely necessary and officers should be armed.
One of Wilkes' first acts in the Fijis was to send a summons to a local great chief, Tanoa. In local custom, compliance would be an acknowledgement of Wilkes' dominance, and Whippy, the local chiefs, and settlers wondered what the response would be. On 12 May King Tanoa arrived from his home on Ambau Island and took up residence in the mbure, or council house. Eager for trade, he gladly signed an agreement for the future safety of United States ships in Fiji. In spite of the treaty, Wilkes was not entirely convinced they would be safe. In setting up his observatory at Levuka, Ovalu, he assigned Marines to it for protection, and on Whippy's advice he hired spies in the king's retinue to keep him informed of any contemplated mischief.
Peacock went to the nearby large island of Viti Levu in order to survey and secure trading agreements with the chiefs there, particularly at the town of Rewa, which had an anchorage. Two days after its departure, Patrick Connell, an Irishman who had settled on Viti Levu came to Wilkes and told him of a particularly treacherous incident that occurred at Rewa in 1834. The American merchant ship Charles Doggett had hired some islanders to help in harvesting and curing biche-de-mer when a rumor began circulating among them that the ship contained valuable objects. In order to obtain them, the local great chief, Vendovi, executed a plot against the ship's crewmen working at the drying house, which resulted in the death of 8 men. The ship's captain forced the return of seven uneaten bodies, but was too late to prevent the consumption of the eighth. On hearing Connell's story, Wilkes sent him to Rewa with a message for Captain Hudson to capture Vendovi. By coincidence, at that time Hudson was conducting a scientific expedition to the interior of Viti Levu, but Alfred Agate, who remained at the shore, was asked by a local chief to paint his portrait. The chief was Vendovi..
After he completed the required survey work at Rewa, Hudson decided to lure Vendovi onto his ship with some other dignitaries, including his brother the king, by offering presents. When Vendovi did not appear, Hudson regretfully informed the king and his suite that they would not be allowed to return to shore until Vendovi was produced. After overcoming some initial alarm, the king agreed, saying that Vendovi terrorized his people as well as white men. Another of the king's brothers and another chief, great rivals of Vendovi, offered to make the trip to Rewa, and the next day they returned with him. Hudson placed Vendovi in chains pending his return to the United States for trial. In spite of their professed need to be rid of him, the king and others wept bitterly in taking leave of Vendovi. Wilkes took it as another of many incongruities of Fijian behavior.
Word of Vendovi's capture reached Wilkes and the town of Levuka within hours. Already, Connell warned him, some islanders were planning to kidnap him to force an exchange of prisoners. Wilkes began carrying pistols and kept armed guards and his faithful dog Sydney nearby.
The surveys continued rapidly. Wilkes method for accomplishing them was to send the various ships out for about ten days at a time with a list of tasks that would take longer than the allotted time. When they reported back to the squadron, he noted what remained undone and re-sent ships out for the remaining items. This way, he felt satisfied that no time was spent in idleness.
When dealing with "savages," Wilkes generally believed that minor crimes committed by them should be ignored, but significant offenses should be punished in accordance with local custom, so that the guilty could fully understand the gravity of their wrongs. As the expedition finished its surveys in the Fijis, he felt compelled to take action twice. First, on 12 July a survey crew lost its boat to an attack of islanders of Vanua Levu. The loss of the boat would seriously hamper surveying, so Wilkes immediately called together a party of men from his and Captain Hudson's ships and rowed more than 60 miles in the evening to the site of the theft. On Wilkes' appearance the next morning, the islanders abandoned the boat, but its contents were gone. In retaliation, Wilkes ordered Hudson to burn the thieves' village. He then again demanded return of the boat's contents and some items were returned. Having thus demonstrated the power of his anger, Wilkes released two hostage chiefs from nearby friendly towns and sent them off with valuable presents, demonstrating the power of his friendship. Word of the incident spread rapidly through the islands.
The second incidence of retaliation took place two weeks later. The survey of the Fiji Islands was nearing completion when Wilkes sent Vincennes and Peacock to Muthuata Island on the north side of Vanua Levu under the command of Captain Hudson, while he took Flying Fish and Porpoise to the western islands of the group. Then, on 24 July, the thing Wilkes dreaded most happened. Islanders killed Lieutenant Joseph Underwood and Midshipman Wilkes Henry as they negotiated for food on the island of Malolo, off the western end of Viti Levu. Their comrades rescued their bodies and brought them to where Flying Fish and Porpoise awaited their rendezvous. Wilkes Henry was Charles Wilkes' nephew, the only child of his sister, and the loss shattered him. He wept openly and it was some days before he could again fully concentrate on his duties. The next day the men were buried on a nearby small deserted island in graves that remained unmarked to prevent the bodies being dug up and eaten. Alfred Agate read the burial service. The day after, a group of sixty crewmen burned the towns of Sualib and Arro and destroyed all the crops and huts between them. A search of Sualib produced some personal property from Underwood and Henry. On the 27 a small group of chiefs led by a woman came asking for peace, but in keeping with Fiji custom, Wilkes rejected it and demanded that all islanders appear before him. When they came, the commander agreed to peace on condition that they bring provisions to Porpoise on the next day, which they did. In his later accounts of the voyage, Wilkes blamed Lieutenant James Alden, commander of the party with not taking proper precautions and even for pursuing the trade, which Wilkes believed was unnecessary.