The first books released covered the Great Sith War (4,000 BBY, or Before the Battle of Yavin). The latter were prequels that covered the Great Hyperspace War, which happened a thousand years earlier.
The Great Hyperspace War was instigated when two Republic hyperspace explorers accidentally crash-landed on the Sith graveyard planet Korriban during the funeral procession of Marka Ragnos. His successor, Naga Sadow, provoked war with the Republic, and installed himself as the leader of the Sith Empire. He fought not only the Republic, but the forces of his chief rival, Ludo Kressh, and was forced to destroy his own fleet to cover his escape. Sadow landed on Yavin IV and constructed vast temples with the labor of his Massassi warriors.
Six hundred years later, fallen Jedi Freedon Nadd arrived on Yavin IV, and learned Sith sorcery from the spirit of Naga Sadow. He took his knowledge and the treasures of Sadow to the planet Onderon, where he used his acquired gifts to install himself as king. His spirit continued to advise his descendants.
Another Jedi, Ulic Qel-Droma, was sent to Onderon to mediate a conflict, where he met the spirit of Freedon Nadd, who told him he would become a Sith Lord. The prophecy came true when the Krath, a secret dark side society, attacked the Republic and injured Ulic with alchemically-treated shrapnel, and then injected him with dark side poisons that would ensure his fall.
Exar Kun left his master, Vodo-Siosk Baas, because his master would not let him learn about the dark side. He went to Onderon, where he learned of Freedon Nadd's tomb. Nadd's spirit told him to go to Korriban, where Nadd tricked him into accepting the dark side. They went to Yavin IV, where Nadd gave him a choice: surrender to the dark side, or die. Kun chose life. After learning about the dark side from Nadd, Kun destroyed him with a dark side amulet.
Exar Kun and Ulic Qel-Droma met on Cinnagar, and their battle was interrupted by the spirit of Marka Ragnos, who declared Kun the Dark Lord of the Sith, and Qel-Droma his apprentice. Together, they waged war on the Republic, stealing Jedi students from Ossus and subverting them to the dark side. Qel-Droma defeated Lord Mandalore, earning the services of the Mandalorian warriors. Qel-Droma attacked Coruscant, but was captured. Kun led a rescue attempt, and killed his former master in the process. Soon thereafter, the Sith Lords caused the Cron Cluster to go supernova, destroying countless Jedi artifacts on nearby Ossus.
Before Ossus was destroyed, Ulic's brother Cay tried to convince him to return to the light. Ulic cut him down in a lightsaber duel and, horrified by what he had done, surrendered himself to his former lover, Nomi Sunrider, when she forever cut off his connection to the Force. Broken, Ulic surrendered to the Republic, and led them to Yavin IV, where Exar Kun committed a ritual that sapped the life from every Massassi on the planet to separate his spirit from his body and bind it to his temple.