Here Be Monsters by John Birmingham

It is 1788 and Lieutenant Watkin Tench of His Majesty's Royal Marines is an officer in charge of transporting over a thousand ne'er-do-well convicts to the great south land. But a mysterious white squall engulfs the Fleet and then it's not 1788 anymore. Not as Tench knew it. A great and ghostly city of the dead appears out of the storm and the men and women of the First Fleet must fight not just for their lives, but for their immortal souls and the very future of the world.