The Sith Inquisitor, a former Slave, starts on Korriban to undergo training to become Sith. It is revealed that the most promising trainee will become the new apprentice to Lady Zash. The young Sith prevails through the early trials and is sent (along with the final apprentice candidate) to the Tomb of Naga Sadow and tasked to uncover its secrets. After discovering a hidden chamber of Tulak Hord and beating its inhabitant, Khem Val, into submission, the Sith Inquisitor returns to the Sith Academy and claims the honor of being Lady Zash's apprentice. Zash instructs her new apprentice to meet her on Dromund Kaas.
Upon arriving in Dromund Kaas, the inquisitor encounters a powerful Sith lord named Darth Skotia, who boasts Trandoshan bodyguards and a body of expensive cybernetics. Skotia is hostile to the apprentice and tells the Inquisitor that he does not know Zash's plans but will stop them, whatever they are. Zash is agitated by this and sends the apprentice across Dromund Kaas on errands that will lead to Skotia's downfall. After recovering a tablet of extreme religious importance to the Trandoshans as a race and procuring an experimental device called the Cybernetic Nullifier, which is designed to negate cybernetic enhancements, the apprentice goes to confront Skotia. Using the tablet to blackmail the guards and the Nullifier to disrupt Skotia's cybernetics, the apprentice and Khem Val are able to mortally wound Skotia, who with his final breaths warns the apprentice that he is next. Zash is ecstatic at her apprentice's victory, but is suspected by a powerful Sith and Zash's superior, Darth Thanaton.
Zash had orchestrated Skotia's assassination so that she simply couldn't be the one who killed him, because she was at the cantina when her apprentice struck him down. However, she had to go to answer Darth Thanaton. Apprentice was a little worried, but when he met Zash at Skotia's old offices, she had received the title of Darth. With that scheme succesful, and Skotia's records now hers, Zash sent her apprentice to the Dark Temple to obtain Tulak Hord's artifact from a Sith apparition. As the apprentice approached the tomb where the artifact was being kept, the apparition appeared. At first it used the Force to throw the apprentice around, but stopped soon, and then explained that he was the Sith Lord Kallig, Tulak Hord's greatest rival, and the apprentice's ancestor. Apprentice believed his story and was allowed to take the artifact, but Kallig adviced him to be careful, due to Sith's deceptive nature. Zash then contacted him and urged him to return back. She had learned that the artifact apprentice found was only one out of five. The other four artifacts had been hidden all over the galaxy. So far Zash had learned locations of the artifacts on Balmorra and Nar Shaddaa. Zash gave apprentice a ship for the search.
On Balmorra, the apprentice had to work with Imperial Major Bessiker to locate the artifact. Major knew where the artifact was located, but the place had become a toxic pit due to the recent war with the Republic. But eventually apprentice managed to obtain it with a serum that made him immune to the toxic's effects. On Nar Shaddaa apprentice had to claim the artifact from a renegade Sith Lord Paladius, who ran a cult. With the assistance of two former members of the cult, the apprentice is able to claim the cult for his own and obtain the artifact. Zash congratulated the apprentice, though she didn't say much thanks.
While resting on her ship, the apprentice got a surprise visit from Lord Kallig. He came to warn him about Zash. Ever since the apprentice left from his tomb, Zash had been visiting the Dark Temple regularly, performing strange rituals in Kallig's tomb. The exact nature of these rituals was unclear even for Kallig, but he was certain they were meant to harm the apprentice. Also, Zash had taken two new apprentices. All this indicated that Zash was planning something that will ruin Kallig's desire to restore his legacy. To that end, Kallig asked the apprentice to go to Korriban and obtain Kallig's mask from a Sith Lord there. The apprentice took Kallig's warning to the heart and obtained the mask. The idea was to prepare the apprentice for Zash's plans. Zash later contacted the apprentice and informed that she had learned the locations of the two remaining artifacts on Tatooine and Alderaan.
While on Tantooine, the apprentice recruits the aid of a former pirate captain, Andronikos Revel, who was mutineed and abandoned by his crew, taking an artifact of Tulak Hord with them. The apprentice teams up with Andronikos to obtain the artifact and also help him get his revenge. On Alderaan, the apprentice learned that the artifact was inside the House Organa Vault, and he needed to eliminate Jedi night Nomar Organa in order to acquire it. He succeeded. After acquiring the artifacts and arriving over Dromund Kaas, the apprentice is heralded by Darth Thanaton, who warns him to be wary of Zash. Also, Lord Kallig appears again and directs the apprentice to Nar Shaddaa to obtain his personal lightsaber from a family retainer.
The apprentice returns to Dromund Kaas and confronts Zash, who is in the Dark Temple wearing a veil. Zash removes the veil, revealing her true appearence to be old and decayed. Zash intended to swap bodies with her apprentice so she may live on. A duel ensues between Zash and her apprentice, with Zash gaining the upperhand and about to complete the ritual when Khem interfers and kills Zash's body. However, Zash's conscience transfers to Khem's body who must share a body with the Dashade. Thankfully, Zash had promoted her apprentice to the rank of Lord so that she would be of higher rank when she possessed her apprentice. The apprentice takes on the role of Lord Kallig, assuming this title to carry on their ancestor's legacy. At the same time, he receives a nice number of followers.
The Inquisitor, now named Lord Kallig, is approached by Darth Thanaton, who explains the importance of Sith tradition and how Zash's ideas flew in the face of that tradition. Thanaton offers to take Kallig as his apprentice and tasks Kallig with entering the tomb of a dead Sith alchemist and acquire his teachings. Upon arriving in the tomb, Kallig is attacked by the ghost of the alchemist, but is saved by the his ancestor who tells Kallig that Thanaton sends those he wishes dead on this suicidal errand. Kallig's ancestor directs them to another Sith ghost, who teaches Kallig an ancient ritual called Force-walking, which allows the Sith to capture a Sith or Jedi ghost, containing them and tapping into their power. Kallig captures the ghost of the one who taught them and the ghost of the alchemist. Kallig's ancestor warns them that this is the last time they shall recieve help from him, and then disappears. Kallig then gathers the alchemist's writings and returns to Thanaton, who is suprised and impressed by Kalligs survival, but upset that it had to come to direct conflict, saying that Kallig's death was a terrible waste. After setting two Sith warriors on Kallig, who easily kills them, Thanaton intervenes directly, using his considerable power and knowledge to defeat Kallig. Believing Kallig dead, Thanaton orders an apprentice to give Kallig an honorable burial before leaving. Zash's former apprentices, now loyal to the Inquisitor, wake Kallig from unconsciousness and warn him that Thanaton has left the planet and that they should leave immediately. It is revealed that the only reason the Inquisitor survived was because of the two ghosts that they had captured. Since the ghosts were already dead, they chained Kallig to this world, preventing him from dying. Kallig flees Dromund Kaas and goes to find more Sith and Jedi ghosts to capture, gaining strength so that the Inquisitor can defeat Thanaton.
Kallig goes to Taris, where the Inquisitor not only captures the ghost of a powerful Jedi, but also corrupt a young Jedi Padawan, Ashara Zavros, who is the descendant of the ghost. Afterwards, Kallig recieves a call from his or her two apprentices, explaing that they hade stolen the key to Darth Thanaton's, meditation chamber, but that Thanaton had sent Lord Cerullion, a Sith in Thanaton's pocket, after them. Traveling to Quesh, Kallig finds his apprentices dead and Lord Cerullion standing over their corpses. Despite being there to kill the Inquisitor, Cerullion is civil and offers his apologies, showing his respect for the Inquisitor. After killing, or gaining Cerulliona as an ally, and retrieving the key, Kallig travels once more to Korriban to view the new stock of acolytes so that the Inquisitor can choose a new apprentice. Overseer Harkun is "welcoming" the acolytes and shows surprise at seeing Kallig, but shows respect for Kallig's new position. Among the acolytes are a human, a Twi-lek, a Kaleesh, and a three-eyed alien. Kallig leaves and resumes the search for ghosts, traveling to Hoth and with the help of Sith archaeologist Talos Drellik, manages to bind the ghost of a powerful Sith Lord to himself. Finally ready to face Thanaton, Kallig returns to Dromund Kaas and enters Thanaton's meditiation chamber, were Thanaton is waiting along with his apprentice. A battle ensues with Kallig killing Thanaton's apprentice and preparing to kill Thanaton. Before they can begin fighting, the Inquisitor draws on the power of the ghosts in him, but cannot control it, blasting Thanaton across the room with lightning and fading into unconcsiousness with the four ghosts mocking Kallig, warning the Inquisitor that they are no longer in control, and that it is their turn to "have some fun."
Having lost control of the ghosts Kallig had bound, Kallig was now in a critical condition. Due to the power had harnessed in such a short time, both Kallig's mind and body had begun to decay. As long as Kallig's condition was like this, defeating Darth Thanaton wouldn't be possible. Zash, with Ashara's help, had already begun to find a cure for Kallig's condition. However, her search had hit a snag when she discovered that the records she had found had been tampered by Thanaton. Fortunately, she knew about Thanaton's private library on Dromund Kaas. Kallig went to the library in order to find the needed information about the cure. Kallig found out that two Dark Lords from the past had experienced similar symptoms. One, Darth Iratus, had experienced body decaying and through extensive search he found a possible cure for his condition on planet Belsavis. The other, Darth Vilus, experienced similar mind decaying and learned about spiritual healing used by the mystical people of the planet Voss. Kallig decided to follow these two leads and set out to search for cure.
Arriving on Belsavis, the secret Republic prison world, which the Empire had recently discovered, Zash informed Kallig that what they were seeking is an ancient healing technology built by the Rakata millennia ago. While searching more knowledge about Belsavis, she encountered mentioning about a group Nikto technicians called The Circle. Their techonological knowledge helps Kallig to locate the Mother Machine, which the Rakata originally built to create entire species for the Rakata to enslave, but later the machine rebelled and they locked it away. Kallig uses the machine to rebuild his body. This new body is strong enough so that the ghosts power no longer can harm it. With his body cured, Kallig was ready to set out for Voss.
Before Kallig was able to go to Voss, he was contacted by Moff Pyron. He had been watching the conflict between Kallig and Thanaton closely and had decided to support Kallig against Thanaton. He also informed him that Thanaton had surpassed his superior, who sat on the Dark Council, and now Thanaton too had become a member of the Council. This was fruitious, because if Kallig can defeat Thanaton, Kallig would become a Dark Council member. Some time ago Pyron had been supervising an ambitious weapon project called The Silencer. The goal of the project was to create a weapon that can incinerate entire fleets with single shot. Thanaton had shut down the project due to his traditionalism, but seeing Kallig rising, Pyron had decided to resume the project without Thanaton's approval. The weapon only required an illegal sensor chip, that could only be found in Nar Shaddaa. Fortunately, Kallig's cult on Nar Shaddaa was the only organisation with a monopoly for these chips, so Kallig traveled to Nar Shaddaa to get one of these chips. Kallig had to dispatch few thieves to get it, but he managed. With Moff Pyron's support ensured, Kallig resumed course to Voss.
Kallig's welcome on Voss was not a warm one. Voss Mystics, who predict the Voss future through visions from the Force, had predicted that Kallig will bring only trouble to Voss. Despite this, Kallig traveled to the Voss capital city, Voss-Ka, to speak with Sith researcher Athelis Kallis for the cure Kallig came to seek. Athelis said, that the Voss have somewhat of a renegade cult called The Shadow Walkers, who walk inside dreams inside their mind. This proved to be exactly what Kallig needed in order to silence the ghosts. Kallig traveled to meet these walkers and after achieving their initiation, Kallig traveled to the Shrine of Healing. In there Kallig learned that the healing ritual is forbidden. The ritual could only be performed in the Dark Heart, located in the Voss Nightmare Lands, an area filled with darkness. But it also required a help of a special dream-walking Gormak, a native species and sworn enemy to the Voss. Only a Gormak like that could use the Dream Rock the ritual needed. With Athelis' help, Kallig was able to locate a suitable Gormak. The Gormak, named Hagrid, agreed to help Kallig if Kallig helps him to leave Voss. The Voss had a strict law that the Gormak must never leave Voss, but Kallig agreed. Together they traveled to the Dark Heart and performed the ritual. The ritual was succesful, and the ghosts inside Kallig's mind were defeated, now under Kallig's total control. Now that Kallig had been cured, it was time for Kallig to destroy Thanaton once and for all.
When Kallig returned to his ship, he was contacted by Overseer Harkun. He informed that the acolytes were about to finish their final trial. Kallig traveled to Korriban in order to obtain new apprentice. It seemed that Kallig's apprentice was to be the Twi'lek acolyte, but then the Kaleesh acolyte, Xalek, beat the Twi'lek to death and handed the required relic to Kallig. Harkun was outraged, but Kallig took Xalek as a new apprentice.
Moff Pyron then informed Kallig that the Silencer prototype was now ready for a field test. Kallig traveled to his ship to oversee the test against a Republic fleet. During test, Kallig declared for the first time that he will be the future of the Sith Empire. The weapon worked perfectly, destroying Republic fleet completely. Even Thanaton could not ignore this success. He contacted Kallig personally, and challenged him into a Kaggath, an ancient Sith duel, where two Sith Lords face off, commanding their own power base and forces. The duel would end after either of the Sith Lords are dead and their forces destroyed. Kallig accepted, and the Thanaton said that the planet Corellia will be their battleground. Turns out that Thanaton had broadcasted the transmission throughout the Empire, with the intention to show, that he is the ultimate Sith Lord. But this also worked for Kallig.
On Corellia, Kallig first had to destroy Thanaton's power base before he could face Thanaton himself. With the help of Moff Pyron and other of Kallig's allies, Kallig eventually destroyed Thanaton's forces and was prepared to face him. Thanaton had gathered a number of Sith to watch the final confrontation between him and Kallig. Though Thanaton still had his power with him, Kallig managed to overpower him. But before Kallig was able to deliver the final blow, Thanaton escaped. Thanaton's former apprentice and now Kallig's ally, Lord Skar, said to him that Thanaton always had this backup plan: should he fail to defeat Kallig on Corellia, he will flee to Korriban and get the Dark Council to destroy Kallig. But because Thanaton had fled like a coward, he had disgrraced the Sith traditions he himself had championed. As a result, Kallig could kill Thanaton with Dark Council's approval.Arriving on Korriban at the Academy, Kallig first dispatched couple of Thanaton's final allies, who were meant to stop Kallig while he addressed the Council. Dark Lords present were mainly Darth Marr, Darth Ravage, Darth Vowrawn and Darth Mortis (others were away or present through holo). When Kallig entered the Council chamber, Thanaton was addressing the Council about that Kallig must be destroyed, because Kallig is corrupt, just like Zash was before. Kallig interrupted him, declaring how he fled Kaggath before it was officially over. Eventually the Dark Council refused to help Thanaton to destroy a mere Sith Lord who seemed impossible for him to kill. Thanaton finally realized that this can only be settled when either him or Kallig is dead. And so they began the duel that would shape the future of the Sith Empire. Thanaton used every trick he had learned over the years, but even they weren't enough for him to destroy Kallig, who had become immensly powerful by the bound ghosts. Kallig used all the power harnessed and eventually broke Thanaton. As he was in his death throes, the Dark Council approached him. He tried to beg them to destroy Kallig, but they had seen enough. Darth Mortis then used the Force to break Thanaton's neck, killing him. Then he presented Kallig his seat in the Dark Council. Darth Ravage opposed first, because Kallig was only a Lord, unworthy for a place in the Council, but Darth Marr then pointed that Kallig had defeated a Dark Council member, and was worthy for a new title and a position in the Council. And so, Darth Marr presented Kallig with a new title, Darth Nox/Imperius. Sitting on his new seat, Darth Nox/Imperius gave his respects to the Council. Marr then said that Nox/Imperius should go to Dromund Kaas to inform all of his followers of this major development. Darth Nox/Imperius returned to Dromund Kaas, took Thanaton's former chambers and gathered all followers to meditation chamber. There, Khem Val announced them their master, the Follower of Kallig and Tulak Hord, and Dark Lord of the Sith, Darth Nox/Imperius.