On Dantooine, Jedi Apprentice Exar Kun curiously asks his Master, Vodo-Siosk Baas, about the Sith, Naga Sadow and Freedon Nadd. Vodo tells him he's too young to learn about the Sith.
In the Empress Teta System, royal Satal and Aleema Keto, students of the Dark Side, stage a coup and take over the government, encasing Satal's own father in molten carbonite.
Jedi Master Arca sends Ulic Qel-Droma and Nomi Sunrider from Onderon to deal with the Ketos.
Before they leave, the spirit of Freedon Nadd appears to Ulic out of a Sith relic and prophesies that Ulic will be a great Sith lord.
On Dantooine, Exar Kun loses his temper when practice dueling with his fellow apprentices, Crado and Sylvar, and they along with Master Vodo fear he is liable to turn to the Dark side.
A month later, Kun arrives on Onderon. He lies and says that he's a Jedi archaeologist, come to examine the Dark side artifacts of Freedon Nadd. Master Arca sees through his lies, but permits him to investigate anyway.
Kun then hires two Dark siders to show him where Nadd is buried on the moon Dxun. Nadd's spirit appears to him and guides him to two scrolls that will tell him where the Sith are now living.
Ulic and Nomi's attack against the Empress Teta System is unsuccessful. The Keto cousins have control of the military and every planet in their system. The Jedi retreat to Deneba to meet with other Jedi and the Republic government to formulate a new plan.
Kun arrives on Korriban, cemetery for the Dark Lords of the Sith. Freedon Nadd's spirit leads him into a trap where a rock slide crushes him. Nadd offers to heal him if he turns to the Dark side. Kun calls out in the Force to Master Baas.
Baas, Crado, and Sylvar follow his call to Korriban, but Kun does not know how close they are. Fearing for his life, he gives in to the Dark side.
Meanwhile, battle droids attack the meeting on Deneba and Master Arca is killed.
Freedon Nadd sends Kun to the Fourth Moon of Yavin, where Naga Sadow made his base after being finally defeated.
When Kun arrives, he is attacked and captured by the Massassi, a tribe of warriors mutated from their Sith ancestors.
Ulic plans to infiltrate the Keto forces and learn how to use the Dark side against them. He thinks he can learn the Dark side without turning to it. He kisses Nomi goodbye and flies off, pretending to be a smuggler.
On Cinnagar, capital world of the Teta system, Aleema knows that Ulic is a Jedi, but decides to let him play his game in order to see what he'll do. She takes him into her service.
On Yavin 4, Exar uses the Dark side to free himself from his captors and gain their loyalty out of respect for his strength. Nadd wants Exar to use Naga Sadow's artifacts and alchemy to create a new body for Nadd, but Exar refuses and destroys Nadd's spirit. He wants power for himself, not to raise Nadd and give him power.
Months later, Nomi travels to Cinnagar and allows herself to be captured in order to find Ulic and see how he's doing. To protect his cover, Ulic agrees to kill Nomi himself the next morning.
On Yavin 4, Exar is experimenting with creating mutant warriors, in true Sith fashion.
Ulic sends message a message to Nomi via a droid revealing that he is working undercover, but the droid is intercepted by Satal, who orders Ulic and Nomi both killed immediately.
Nomi uses Jedi battle meditation to turn her guards against each other, then escapes and contacts Cay and Tott for backup.
Ulic escapes as well and then kills Satal out of anger for killing Master Arca. He thus gives in to the Dark side and refuses to go with his allies when they arrive.
Ulic again refuses to go with them and the Jedi withdraw. Exar Kun then attacks, but an ancient Sith dark lord appears to them in spirit and names Kun as the new Dark Lord, and Ulic as his Apprentice, marking both of their foreheads.
Kun and Ulic then agree to conquer the galaxy together.