Alert recommissioned at Chatham on 20 August 1878 under the command of Captain Sir George Strong Nares for a survey of the Strait of Magellan. On 12 March 1879 Captain John Maclear took command, and under him she went to Australia Station and the Pacific. She was employed in surveying, but the presence of Doctor Richard Coppinger, her surgeon, ensured that she also made a huge contribution to the field of zoology. Coppinger, who had also served in the Arctic expedition, was an accomplished naturalist and his collections from the period 1878–1882, which included indigenous cultural artifacts purloined, as he admitted, from Mutumui sites on Clack Island,Peter Sutton,'The Flinders Islands and Cape Melville people in history,' Jean-Christophe Verstraete, DSisane Hafrner (eds.), Land and Language in Cape York Peninsula and the Gulf Country, = John Benjamins Publishing Company 2016 p.90 added 1,300 species to the National Collection.From the preface to the Report on the zoological collections made in the Indo-Pacific Ocean during the voyage of HMS Alert, 1881-2, published by the British Museum, 1884 Alert paid off at Sheerness on 20 September 1882.
