A Jedi named Exar Kun is, without permission, viewing a recording in his master's holocron. What he sees is Naga Sadow, an exiled dark lord of the Sith in retreat from Republican ships. As they fly between a double star, Sadow and his followers escape, not only destroying the Republicans behind but also the complete Star System. The holocron also tells him that there was only one dark lord at a time and an envious dark Jedi named Freedon Nadd, who was refused the title, retreated to Onderon where he could dominate its people and claim the dark lord title himself.
As Exar Kun continues to ask questions to the holocron, his master Vodo-Siosk Baas, enters the room and urges his student to turn the holocron off. "These recordings are for Jedi Masters only and you are not ready to learn about such things."
Meanwhile, in the Empress Teta System. Lord and Lady Keto are carrying out an annual inspection on a mining station when their son, Satal, along with cousin Aleema and tutor Korus, make an unexpected arrival. As Lord Keto questions Korus bringing these children here, being a breach of protocol, he discovers that the tutor is just a pawn in this. Showing they are adept in Sith magic now, the cousins reveal what is wrong with Korus, that he now has a snake-like beast where his tongue used to be. Frightened and concerned, Keto calls security only to find his attempt to remedy the situation in vain as he, his wife and everyone else opposed to Satal and Aleema, become terrorised by Sith magic. Those who don't die from catatonic shock are lowered in a vat of molten carbonite including Satal's mother and father, the rulers of the Empress Teta System.
Having already established their army as the Krath, Satal and Aleema claim themselves as the new rulers of the Empress Teta System and celebrate with a feast. Here poor old Korus, who's mouth has been forced shut, is serving wine when he has a little accident and as a consequence, meets his doom
On Onderon, the Jedi Knights who helped remove the dark side from this planet are enjoying a much-deserved holiday. Their rest, however, is about to end as Master Arca informs them that a political coup in the Empress Teta System seems to be connected to the Freedon Nadd Uprising. He sends Dace Diath, Qrrrl Toq, Oss Wilum and Shoaneb Culu to Ossus to inform other Jedi and Republic leaders, who are also joining the fight, of the dark side powers they witnessed in the Freedon Nadd Uprising. Arca tells Nomi Sunrider that once he has given her a lesson of Jedi battle meditation, she is to travel with Ulic Qel-Droma to the Empress Teta System and together lead the Jedi effort. While Master Arca trains Nomi, brothers Ulic and Cay decide to check out the Sith gear that King Ommin collected and Ulic comes across the spirit of Freedon Nadd once more. Nadd warns him not to interfere with the work of the dark side but also suggests that Ulic will be one of the great ones...
On Dantooine, Jedi Master Vodo is monitoring two of his students in a lightsaber duel, Exar Kun and Crado. Crado is no match for Kun, more importantly he knows it which is half the reason why he loses. Sylvar however, another of Vodo's students and Crado's lover, is more determined to fight Kun. As they duel, tempers rage and Sylvar leaves a fierce mark on Kun's face after clawing him. Kun urges Sylvar to rise and continue fighting but she refuses claiming he is no Jedi. Kun, in a fit of rage, attempts to strike Sylvar but Vodo intervenes. Master Vodo instructs his fierce student that anger is not the way of a Jedi and challenges his student to a duel which Kun earnestly accepts. During the duel Vodo, more experience, finds Kun's balance point and knocks him down to the mercy of his master's staff. Kun, however is not finished and reaches out with the force for another lightsaber. He rises once more and the battle between master and student is ended when Kun breaks Vodo's staff. "A Mighty Jedi... two lightsabers against my poor stick. Exar Kun, you are the most formidable student I have ever had..." Vodo proclaims but he senses a darkness in this student and it concerns him.
On Onderon, a Jedi outpost is being converted from an ancient starship which once belonged to Freedon Nadd. While overlooking the completion of the outpost, supervisors Cay Qel-Droma and Tott Doneeta are awaiting a visitor, a Jedi archaeologist named Exar Kun. Kun, who has left his master Vodo-Siosk Baas, is determined to see Sith artifacts which belonged to Freedon Nadd. When he arrives Cay informs him that Master Arca has ordered the artifacts shipped directly to Ossus. Kun, however, insists he must see them before this occurs and is thus introduced to Arca. Arca refuses to help though, claiming he's no archaeologist and that his fascination with the dark side has already led him into lying. "You are not welcome on Onderon, Exar Kun!". Despite this Kun returns to his ship and flies into the city of Iziz.
Meanwhile, the planet Koros Major, the only planet left in the Empress Teta System to oppose Satal and Aleema's military coup, is now under attack. Using her newly acquired sorcery and mystical powers from studying Sith magic, Aleema manages to play mind tricks on the enemy. As they continue their attack however, the joint peace keeping fleet of the Galactic Republic and the Jedi Knights emerge from hyperspace. On board the Republic command ship (the Reliance) is Captain Vanicus with mission overseers, Jedi Ulic Qel-Droma and Nomi Sunrider. Ulic orders a cease-fire message to the new Tetan leaders but they receive no reply. Aleema, however, sends a message of her own via Sith magic and creates huge "Space Grazer" beasts which hover over the Republican ships. As Ulic and the other commanders panic, these thought-to-be-extinct creatures used to prey on galactic space traffic, Nomi Sunrider channels out through the force and realises these beasts are nothing more than illusions.
In the city of Iziz, Onderon, Exar Kun comes across two Freedon Nadd preachers who are being met by a rather hostile crowd. Kun intervenes as the crowd becomes an angry mob and makes a deal with the two Naddists. Following this the two agree to go with Kun to the Dxun moon where Nadd's remains are kept. Upon arrival and without too much difficulty, Exar Kun enters the tombs of Freedon Nadd, Queen Amanoa and King Ommin. The spirit of Nadd appears and instructs him to take two scrolls hidden inside the corpse of the dark lord. Kun is told that the scrolls were written by Nadd's master and they will guide him to the last home of the Sith. Leaving the tomb, Kun finds himself at gunpoint by the two Naddists, Nebo and Rask, but Kun is quick to strike them, too quick and with so much anger that it frightens Kun himself in letting hatred flow through him so rapidly. Meanwhile in the battle over Koros Major, the republic has accepted the grazers to be nothing more than hallucinations and begin attacking the Krath command station. Aleema, having underestimated the Jedi, plans with Satal their second attack. As the Republican fleet continue their attack, a large number of enemy ships come into sight. Vanicus orders his crew to battle stations but Nomi senses the ships are another illusion and informs the crew as she herself attempts to get inside Aleema's head. On the Krath station, Aleema feels this intrusion and stuggles to maintain the illusions she has created. As the hallucinations disappear however, the Republican fleet realise they've been tricked - half the enemy ships are real. Defense shields aren't quick enough to stop the Krath chaos ships which plummet into their enemy, including the Reliance where Ulic is badly injured. As Nomi conforts her colleague she curses herself for falling for the trap. In the meantime, Captain Vanicus orders a retreat.
As the Republican fleet excavuates the Empress Teta system, light-years away Exar Kun, who has been studying the scrolls given to him by Freedon Nadd, flies his starship into the atmosphere of Korriban, the final resting place of the Sith.
Following the Jedi/Republican task force's failure against the Krath in the Empress Teta System, a special gathering is arranged for which thousands of Jedi Masters and Jedi Knights converge on the planet Deneba to discuss alternative ways to bring Sith magicians, Satal Keto and his cousin Aleema, to justice.
Meanwhile, on Korriban, Exar Kun continues his research into the Sith and finds himself surrounded by immense darkness. He is attacked by skeletons who come to life by the mere power of dark side energies and it scares him a little. After defending himself, the spirit of Freedon Nadd appears and leads him into a cave which is the opening to a great temple. As Kun enters, however, the entrance collapses.
As the assembly commences on Deneba, chairman Jedi Master Odan-Urr calls Ulic Qel-Droma and Nomi Sunrider to the stage. Ulic suggests an alternative way of defeating the Krath rather than overwhelming military force - that someone joins the Krath, learns the secrets and defeats the dark-siders from within. This plan of Ulic's is met with strong debate with other Jedi claiming it will only lead that person into the dark side.
On Korriban, Freedon Nadd leads Exar Kun to a great crystal which conceals the spirits of Jedi Masters who opposed the ancient Sith. Nadd believes it is time to release these souls and to liberate Exar Kun. He shatters the crystal annihilating the spirits which in turn smashes Kun's bones in a hundred places. As Kun lies helpless he pleas to Freedon Nadd for help but Nadd claims the only way of healing is to accept the dark side of the force. Stretching out through the force, Kun seeks out his master Vodo-Siosk Baas, who is aboard his spacecraft approaching Deneba. Vodo attempts to help his apprentice but Freedon Nadd intervenes and the great Jedi Master is not powerful enough from this vast distance to save his student. Kun, slowly dying, is forced to surrender to the dark side. He finally accepts and while the dark side of the force begins to heal the broken body of Exar Kun, the transition to the dark side is felt throughout the galaxy.
In the meantime, on Deneba, the Jedi council stands motionless after sensing Exar Kun's turn to the dark side. Suddenly, they are attacked from air and by land. A Tetan corsair releases a barrage of life pods which strike the surface of the planet like meteors and then reveal an army of war droids. Meanwhile the servant droids among the Jedi meeting begin to attack. The Jedi defend themselves well but when Master Arca averts his senses into saving his apprentice, Ulic, he is struck from behind. As Ulic listens to his Master's dying words, Exar Kun, on another world, receives life once more.
Freedon Nadd leads his new apprentice through the ancient temple where Kun, who realises he has acquired new strengths, is told to test his commitment to the dark side. Guardian creatures attack him and Kun realises, as he tries to reach out with the force, that the lightside is blocked - he is helpless, unless he reaches out with anger, with the dark side. Doing this, he acquires his lightsaber and destroys the creatures. The spirits overwatching approve of Exar Kun and claim "He is ready!" Despite this Exar Kun claims he will never be seduced by the dark side but Nadd tends to disagree - "oh, but you already have, you already have!". Kun is sent to Yavin four to continue his research....
On Deneba, as the battle ends, Cay and Tott learn that the attack was planned by the Krath. Meanwhile, Ulic still sits at the spot where his master was killed, blaming himself, when Nomi Sunrider comes to comfort him. He tells her that he plans to infiltrate the Krath himself and bring the dark-siders to judgment but Nomi urges him not to go, that he who takes up the path of the dark side is no longer a Jedi and will become infected with darkness.
Exar Kun arrives on a moon of Yavin with Freedon Nadd's spirit before him. Nadd tells him that this is Naga Sadow's ancient Sith world and to beware of the Massassi who protect the great temples for they are decendents of ancient Sith. Kun, sick and tried of this "old dark side ghost", tells Nadd to leave him alone. Nadd agrees, while Kun, feeling the strength of the dark side on this moon, is attacked by the Massassi and rendered unconscious. Zythmnr, the temple priest of this race had emerged from twelve years of solitude to witness the arrival of this man, knowing this is the one they have been waiting for...
Meanwhile, on the planet Ossus, Ulic Qel-Droma is given a book containing the history of the Empress Teta system by Master Ood. Ulic is planning his trip to the Tetan system to infiltrate the Krath but before he goes, Ood sends him to Master Odan-Urr for advice. Odan-Urr shows him a Sith hologram which reveals a Jedi in the past who felt he could conquer the dark side from within, but the dark side seduced him entirely and he turned to anger - killing his own Master. Ulic is slightly offended about being shown this and leaves the company of the two wise Jedi Masters, who he believes are complacent. Ulic farewells his brother, Cay, (who wants to go with him but Ulic declines) and in the morning, before leaving, he embraces and kisses his new lover, Nomi Sunrider, who also warns him not to go. Despite everyone's notion that this is a bad idea, Ulic aboards his Kestrel Nova and heads off for revenge...
On Yavin Four, Exar Kun awakes and finds himself tied to a pole in the middle of an arena along with many other prisoners. He senses dark side energies which become stronger and stronger and then to his dismay, a huge beast (one of Sadow's ancient alchemical creations) arrives on the scene, attacking the prisoners.
Ulic lands on Cinnagar, the ruling city of the Empress Teta system, but his arrival is not as secret as he hoped as Satal and Aleema sense he is a Jedi. Though Satal wishes him dead immediately, Aleema believes she can can use him. The following day, a public execution ceremony takes place in which resisters to the Krath are thrown into a vat of molten carbonite. A group of assassins, however, have planned to attack Aleema and as they do so Ulic comes to her rescue. What he doesn't know is that she planned the whole thing to test Ulic's allegiance.
Yavin Four, as Exar Kun becomes the next prey for Sadow's beast, Nadd visits him once again and tells him that he will die unless he uses the dark side of the force to summon the amulet. Reaching out in rage and finding he can speak the Sith tongue, Exar Kun pulls the amulet to himself and upon wearing it finds himself at the helm of immense dark side energy. He destroys Sadow's creature and is worshipped by the Massassi. Nadd is pleased with Kun's work and tells him of the next stage, "Now, my son, we will begin the alchemical work, so that I can be reborn into a new body." Kun, however, has other ideas and decides to annihilate the spirit of Freedon Nadd once and for all by using the amulet against his master. As Nadd dies a second time, he reaches out in desperation to other dark siders (including Satal and Aleema) and warns them of Exar Kun.
Ulic Qel-Droma hangs as a prisoner deep beneath the iron citadel on Cinnagar. As cousins, Satal and Aleema approach, they argue about the future of this Jedi knight. Satal wishes him dead but Aleema claims he will help them and even teach them a thing or two. Keto decides to test him by injecting the young Jedi with Sith poison. The poison acts quickly, pulling Ulic out of delirium and an impulse of force energy blasts him free from his bondage. Aleema curses Satal claiming he nearly killed their prisoner but Aleema now has her way, Ulic is hers to do as she pleases.
On Yavin Four, Exar Kun, now the leader of the Massassi (the natives of this moon), has ordered his followers to build great Sith temples while he himself seeks to learn more of Naga Sadow's Sith magic. Upon venturing deep within the surface of Yavin Four, Kun finds not only Sadow's spacecraft but also a hidden chamber which contains the appartus of Sith alchemy.
Meanwhile, the Nebulon Ranger - with its passengers Cay Qel-Droma, Tott Donetta and Nomi Sunrider - arrives above the planet of Cinnagar. Nomi is planning to contact Ulic, whom she cannot reach within the force, and find out how he is. Though Tott and Cay are not too sure about this plan of hers, they agree to help her. As Nomi heads to Cinnagar in an escape pod, the Nebulon Ranger hides in the shadow of the Tetan moon awaiting her orders.
Upon landing in Cinnagar, Nomi realises that the only way to make contact with Ulic is getting herself arrested. She ignites her lightsaber and is immediately attacked and taken captive. She is taken to the Krath war room where Ulic Qel-Droma is trying to prove his allegiance to the Krath via a skeptical Satal Keto. When Keto learns that Ulic and Nomi know each other he plans to test Ulic's fidelity to the Krath by getting Qel-Droma to assassinate his fellow Jedi companion. Ulic agrees to do this at dawn much to Nomi's dismay. Ulic can only hope that Nomi can get out of trouble on her own.
On Yavin Four, Exar Kun is playing a little experiment. Using the Massassi Priest, Zythmnr, as his guinea pig, Kun is testing some of the Sith alchemy he has been studying to transform the priest into a greater being. The experiment is a success and Zythmnr emerges much larger and much powerful than before. Kun, as Sadow did in the past, plans to create armies with these monstrosities.
Returning to Cinnagar, Ulic plants a message for Nomi into a servant droid. The message tells her to return Ossus and wait a little longer, he needs more time. As Ulic finishes the recording, Aleema enters and the two become intimate. Meanwhile, Satal orders the droid to his attention and finds the hidden message. Destroying the droid, and hence the message, Keto orders his assistant (Norgor) to bring Nomi Sunrider to him and to assassinate Ulic Qel-Droma.
In the dungeons of Cinnagar, Nomi is intruded upon by several guards. Using her Jedi Battle Meditation, she turns the guards against each other and while they brutally fight, she makes an easy escape. Finding a comlink she calls for Cay and Tott's assistance. Meanwhile as Ulic awakes from his slumber with Aleema an assassin enters the room and attacks him. Ulic defends himself well bringing down the assassin whom Aleema informs was Satal's slave, she also lets out that it was her stupid cousin's idea to attack Deneba.
Elsewhere, Tott and Cay meet up with Nomi and plan to rescue Ulic but Satal Keto and his men interupt. Ulic suddenly appears next to Satal and informs his brother that this is the man who killed Master Arca. The duel between Ulic and Keto does not last long, the Jedi is easily the victor but as Satal Keto dies Ulic feels a change within, he has given himself to anger which in turn ignited the Sith poison Satal had injected. Cay attempts to persuade his brother to leave with them but Ulic refuses and unleashes a powerful dark side energy. The three Jedi (Tott, Cay and Nomi) retreat to the Nebulon Ranger and make it safely to hyperspace but during their escape they feel that Ulic is lost to the light and he will never be the same.
As Ulic apologises to his friends through the force (knowing he is now on the dark path), Exar Kun, plans to leave Yavin IV and head for the Empress Teta System where he will track down the Freedon Nadd students and destroy them - there can be only one.
Jedi knights, led by Cay Qel-Droma and Nomi Sunrider, are planning an important mission to Cinnagar where they are attempting to rescue Ulic Qel-Droma and defeat the Sith magicians. After receiving permission to carry out their plans by the great Jedi Masters (though, they are warned that if Ulic has chosen the dark side they cannot intervene, nor bring him back) the Jedi knights Dace Diath, Shoaneb Culu, Oss Wilum, Qrrrl Toq, Tott Doneeta, Cay Qel-Droma, and Nomi Sunrider, along with friend Oron Kira and his beast-riders, commence their journey to the Empress Teta System.
Meanwhile, Exar Kun and his Massassi escorts have just arrived on Cinnagar with intentions to kill potential rivals Ulic Qel-Droma and Aleema. As Kun heads towards the citadel, Aleema gives her lover, Ulic, a Sith talisman which belonged to her cousin, Satal. The amulet Kun wears has a connection to this talisman and begins to glow. Kun now knows for sure the dark-siders on this world are a threat to his work but as he plans to enter the citadel a fleet of attackers enter the sky.
The attackers being the Jedi knights from Ossus carry out their plan flawlessly and as they approach the royal citadel, Cay, Nomi and Qrrrl Toq climb aboard the Onderonian warbeasts they brought with them and enter the palace. There they are met by Ulic and Aleema. Protecting her lover, Aleema casts a Sith spell against Nomi but the Jedi is too strong in the force that she sees right through the illusions. Outside, the Jedi attack force continuing to rotate around the palace come under attack by Tetan chaos fighters. As Oss Wilum fights he is drawn to a man walking below, a man who is very powerful in the force, his name - Exar Kun.
Inside the royal quarters Nomi, Cay and Qrrrl attempt to take Ulic back with him despite his refusal. Nomi then realises that they must leave him, they must obey the Jedi Masters and allow Ulic's life to run its own course. Cay, though refusing to allow his brother to become part of the dark side, finds his attempts futile and together with Nomi, Toq, and the other Jedi knights, leaves Cinnagar. As Ulic and Aleema watch on, the fallen Jedi realises his lover now knows his plans, but Aleema claims she knew from the beginning and enjoyed the idea of having a worthy adversary.
The two are about to retire for the evening when another intruder enters the royal quarters. As Ulic ignites his lightsaber, Aleema unleashes her Sith powers towards the stranger but her magic is not match for Exar Kun who strikes her down with the power off his amulet. Kun and Ulic then converge in a lightsaber duel. Both expert swordsmen, the battle continues on at a fierce rate when suddenly they are interupted by a dark spirit emerging from Kun's amulet and Ulic's talisman. His name is Naga Sadow (though not revealed in this comic) and he tells the two feuders that they must join forces in order to bring the Sith back to prominence. He appoints Exar Kun as the Dark Lord of the Sith and Ulic Qel-Droma as Kun's first and foremost apprentice.
As Aleema regains consciousness she witnesses an astonishing sight, Ulic and the intruder are rippling with dark-side power, more than she ever had, and are now friends. Exar Kun: "Let it be so, Qel-Droma... the ancient Sith have spoken. Together we will bring down the galaxy!"; Ulic Qel-Droma: "Yes. Let it be so.".