Following Pellew's replacement by Rear-Admiral William O'Bryen Drury, "Doris" was sent to serve in the Strait of Malacca, on a mission to obtain a working relationship with the Spanish government in the Philippines. For his successful efforts he was given command of the frigate HMS "Caroline" in 1809 and the following year was given command of a squadron with which to attack the Molucca Islands on a free commission. Sailing to the well-defended island of Banda Neira, Cole planned an audacious attack on 10 August 1810, his troops storming the fortress and successfully capturing it. The following year he took a leading role in the planning of the invasion of Java, which was successfully completed under Rear-Admiral Robert Stopford. For his services, he was knighted in May 1812, awarded a specially minted medal and given an honorary doctorate by the University of Oxford.