Nagasaki is a Japanese port in the far south of the country.
In the Series
John Fletcher was piloting the Alexandria was heading there in The Way of the Warrior, but the ship got shipwrecked and attacked by the Wakou. At the end of The Way of the Dragon, Jack was heading for Nagasaki. Finally, in The Ring of Sky, Jack reached the port and sails home to England.
It was the port most commonly visited by European explorers and missionaries because it was the closest port to the Indian Ocean from which most European sailors arrived. It was also one of the closest ports to China which was much more widely know to Europeans than Japan. Nagasaki was connected to the Japanese capital of Kyoto via the Tokaido Road. During the Kamakura purges, in which all gaijin were executed or expelled from Japan, it became a safe haven for persecuted Europeans. Later, during World War II, Nagasaki would be nuclear bombed by the Americans in order to force the Japanese Empire into surrender and intimidate the Soviet Union.