Accounts by those involved in the expedition vary, but around midnight on 11 June the expedition split, with Quiros' flagship, the San Pedro y San Pablo apparently forced to turn back by a mutinous crew. They reached Acapulco in November 1606.
Torres failed to find the missing vessel, waited another fifteen days at Espiritu Santo and then opened his sealed orders, which nominated Quiros's second-in-command, Don Diego de Prado to take command and search for land as far as 20°S.
Prado seems to have been happy for Torres to assume de facto leadership of the remaining two ships in the expedition.
Torres took them south to 21° just under 500 km from the Australian coast without finding land and steered for Manila. They sighted land, probably an island of in the Louisiade Archipelago, south-east of New Guinea on 14 July 1606, but were unable to weather the eastern end of New Guinea.
As a result, the two vessels followed the south coast of New Guinea, and passed through Torres Strait, proving that New Guinea was not the northern extremity of a southern continent.
Torres reached Manila on 22 May 1607, and we know nothing of what transpired from there.
The report of his voyage seems to have been filed and forgotten until the British occupied Manila in 1762. After that, his accounts were seen by Admiralty Hydrographer Alexander Dalrymple, who provided a sketch map which included the Torres voyage to Joseph Banks, who would have passed the information to James Cook.