Wilkes in Vincennes arrived at Valpariso on 15 May to find Relief and Peacock waiting for him. He knew of Peacock's intentions, but was furious to find Lt. Long in Relief had acted contrary to orders. Long had won the admiration of his crew for his calm manner and excellent ship handling in saving his ship from the rocks at Noir Island, but on hearing the story Wilkes faulted him for neglect and abandoning orders, and determined to return him to the United States as soon as possible. As soon as Relief was repaired, Wilkes sent it north to Callao, Peru to have it fumigated to destroy the rats that were eating away at the supplies it carried. He also continued a reorganization of officers that he had begun at Orange Harbor, transfering those he wished to be rid of to Relief. Meanwhile, the crew received shore leave and some of the officers and scientists made an inland excursion to Santiago.
As soon as they were able, the other ships moved up the coast to Callao, the port city for Lima. Anxious over the absence of Sea Gull, Wilkes left Lt. Thomas T. Craven at Valpariso to take command of it, or failing its return, to take passage for the United States. He also sent notice to Commodore Nicholson at Rio to make a search for the vessel.
While the squadron spent a month at Callao completing preparations for their venture to the Pacific islands, a group of scientists explored the surrounding terrain and Wilkes took the opportunity to implement his reorganization. He placed on Relief some officers and men who he believed were impediments to the mission or personally opposed to him. He then detached the ship and sent it home via Honolulu, Sandwich Islands (Hawaii) and Sydney, New Holland (Australia) where it was to leave caches of supplies for the expedition. Feeling lightened of a burden, Wilkes looked forward to more timely progress. In his reorganization, he placed the scientifics Agate and Rich on board Peacock.