Cooke then served as an aide to Sir George Keith Elphinstone, who was appointed governor during the ensuing Siege of Toulon, and escaped in December when the city was evacuated ahead of the advancing Republican armies. For his services, Cooke was promoted to post captain, participating at the Siege of Calvi under the command of Captain Horatio Nelson. In 1794 Cooke was given command of the 40-gun frigate HMS "Sybille", recently captured from the French at the Battle of Mykonos. He took "Sybille" to the Cape of Good Hope and then eastward into the Indian Ocean as a convoy escort under the command of Rear-Admiral Peter Rainier. In 1798, accompanied by HMS "Fox", "Sybille" entered the port of Manila in the Spanish Philippines disguised as a French ship and convinced the defenders to come alongside peacefully, thus seizing three gunboats and 200 prisoners of war, who were later released after being questioned. The Raid on Manila secured a considerable amount of valuable information.