The Sith Navy was created by the Sith Council over a year before the War. Originally, it was under the command of Lord Kracor who organized it into a working organization. Shortly before the Breaking of the Corellian Blockade, Kracor's home empire was attacked by the Galactic Alliance and he returned to rescue his wife and other captives.
Bastilla took command of the Navy for the next few months and managed to hold it together against the overwhelming numbers of the Galactic Alliance. Eventually though, she was forced to turn her attention elsewhere and placed Lord Bane in command of the fleet. Bane was later put in command of the Navy and led the charge against the Galactic Alliance. After some time, command was returned to Kracor once again until the end of the Galaxial War. The Navy underwent one last command change to Tress.