The newest, most advanced destroyer in the Japan Maritime Self-Defense Force, the JDS Mirai, sets sail from Japan on a training exercise with the United States Navy. Enroute, they encounter a strange meteorological anomaly. The Mirai loses contact with her sister ships and finds herself sailing by the unmistakable silhouette of a Imperial Japanese Navy battleship, the Yamato.
The Mirai eludes the Imperial Japanese fleet and, reluctantly, the crew realizes that they have traveled sixty years into their past to the early days of World War II. Their first desire is to return home, and to ensure that they have a home to which to return they decide to do nothing that will change history. That good intention does not last long, however, and gradually they are drawn into the conflict, though they continue to refuse to choose one side over another. The struggle of the crew from a modern, peaceful, and wealthy Japan to resist the nationalistic appeal of defending their country, knowing that in this time it is ruled by a brutal, totalitarian and militaristic government is the central theme of Zipang. Their rescue of a Japanese navy officer from the past, Lt. Commander Kusaka, who would have perished in the normal timeline, causes unstoppable and devastating changes in the past when he seeks to create a stronger Japan no matter what the cost.