Overview:

Reconstituted by the near-limitless production capability of the Star Forge, the Sith military had the manpower and personnel to mount a full scale assault on the Galactic Republic. The opening battle of the Jedi Civil War was the Battle of Foerost in 3959 BBY, during which the Sith military captured a significant portion of the Republic Navy's fleet at the Foerost Shipyards. Significant segments of the Republic Military defected to the Sith military, enabling rapid advances with minimal casualties. Logistics support and materiel was provided by agreement with the Czerka Corporation. 

During 3958 BBY, Republic Navy Admiral Saul Karath defected to the Sith Empire. One of his first acts as a Sith admiral was to lead the Bombing of Telos IV. The orbital bombardment was unprecedented in its scale, killing millions and served to send a message to the Republic on how far the Sith were willing to go. In 3957 BBY, Darth Revan was captured by the Jedi, however Darth Malak attempted to kill his former master and sized leadership of the Sith Empire and its military. 

Following Malak's assumption of leadership, the military campaign shifted from strategic conquest, with an emphasis on preserving industrial capacity, to one of total war. In 3956 BBY the Sith military captured Taris and launched an attack on the Republic Hammerhead-class cruiser Endar Spire in an attempt to neutralize Bastila Shan. Following Shan's rescue by Revan, who had his brain wiped and was now working for the Republic, Darth Malak directed the destruction of Taris which killed billions of citizens and shocked the galaxy. 

Sith forces engaged with Revan during his quest for the Star Maps during his raid on the Manaan Sith Embassy. At Darth Malak's direction, the Sith military launched an attack on Dantooine, executing orbital bombardment and surface operations, destroying the Jedi Enclave and occupying the planet. Sith forces also briefly captured Revan before he escaped after killing Admiral Karath aboard the Interdictor-class cruiser Leviathan. Revan proceeded to eliminate the Sith Academy on Korriban while finding the last Star Map. The Battle of Rakata Prime marked the end of the war, with the death of Darth Malak, the destruction of the Star Force, and fracturing of the Sith Empire and its military. General uprisings occurred, such as the Ahto Uprising, as worlds revolted against Sith rule.