Believing the Empress Teta system is in chaos, the masked warrior clans of Mandalore decide to attack and claim the worlds for themselves.Ulic Qel-Droma, currently planning an attack on the Republic, does not have time for this and demands Mandalore (the leader of this attack) to surrender. Mandalore, whose army is far more advanced than that of the Tetans, offers Ulic an alternative to space fight. He and Ulic will battle it out, one on one, on Mandalore's home planet. If Mandalore wins he will claim the Empress Teta System, if Ulic is the victor than Mandalore's army will serve the fallen Jedi. Both agree and plan their duel.
Meanwhile, on the planet Ossus, Exar Kun has rounded up several Jedi knights, including Cay Qel-Droma and Oss Wilum, and attempts to persuade them to be his disciples by showing them his amulet and informing them that he was the one who innolated the spirit of Freedon Nadd.
On Kuar, Ulic prepares to battle Mandalore. Ulic, equipped with his lightsaber and as a rule by Mandalore, not permitted to stand on a mount nor solid ground is up against Mandalore, who's weapon is the Basilisk war droid. As the battle begins it appears evenly matched. Ulic manages to knock Mandalore off his droid and the two then converge in sword to sword combat. In the end though Ulic wins and Mandalore cedes his warriors to the Jedi, preparing to die. Ulic, however, will not kill him as he has something better in mind for the warrior.
Returning to Ossus we find Nomi Sunrider in the company of great Jedi Master Odan-Urr who is teaching her more about Jedi Battle Meditation. Nomi asks if the Dark Side can use this technique and if so, how can she overcome it. Odan-Urr tells her it is possible but "you must use your Jedi abilities to take power away from an opponent rather than to inflict pain". He warns her though - "It it the most devastating attack possible using the powers of the light side. To block a Jedi from the force - even a dark jedi - is a terrible thing." He speaks from experience having to use the technique in the days of the fall of the Sith Empire and shows Nomi the Sith holocron that he captured which can only be accessed by a dark lord of the Sith.
Meanwhile, Exar Kun has left his assembly of curious Jedi knights as they think about joining him, and currently waits outside Odan-Urr's dwellings to reclaim something he believes is his. After Nomi and her daughter, Vima, farewell Odan-Urr for the evening, the Jedi Master notices the holocron beginning to glow and suddenly it flies from his hands and into those of Exar Kun. Odan-Urr tries to block out the power of Kun but realises he is too old to stop it, Kun attacks him with the dark side, and sadly, Odan-Urr is no more. As Kun kicks the remains of Odan-Urr, the Jedi knights who have chosen to join him arrive on the scene. Oss Wilum notices the robe and staff of Odan-Urr and enquiries. Exar Kun claims it was the Masters's time but before he died he honored Kun as a Jedi Master and gave him the Sith holocron as a gift.
With Mandalore's strong fleet at his side and Aleema's powerful Sith illusions, Ulic and his armies attack a great Republic shipyard and succeed almost instantly. Taking control of the shipyard and claiming three hundred new warships, Ulic plans his next move, Coruscant - the heart of the Galactic Republic. Exar Kun transmits a message on board with the news that he has acquired twenty Jedi Knights ready to commence training. Kun learns of the Coruscant plans and suggests that Ulic and his armies wait but Ulic is determined to prove the Republic is weak and vulnerable.
Captain Vanicus and his crew arrive at the great shipyard of Foerost after learning of an attack. What they find is ruins, most of the ships have been stolen and everything else has been destroyed. Searching through the dismantled shipyard they discover that the security system recorded the pirates. As Vanicus watches the recording he recognises one of the men to be Ulic Qel-Droma. Ulic, obviously knowing he was being recorded, mentions to Mandalore that they are ready to attack Kemplex Nine (though he is actually planning to attack Coruscant).
Meanwhile on Coruscant, Master Vodo, along with several Jedi knights, arrive just in time to hear news from Vanicus that the leader of the terrorist attacks on Republican shipyards is none other than Ulic Qel-Droma. His brother Cay finds it hard to believe but Master Vodo says this goes further than a renegade Jedi and that Ulic is merely working for Exar Kun, Vodo's apprentice. Vodo realises he must find them. As the great Master speaks however, a large fleet emerges from hyperspace and begins attacking the planet.
On the fourth moon of Yavin, Exar Kun has brought twenty curious Jedi along with him for further training. What they don't realise is that Exar Kun has brought them here to convert them to the dark side. By releasing the Sith holocron he has acquired, Kun unleashes shards of crystals which find their ways into the unsuspecting Jedi, filling them with powerful Sith magic and evil. As Crado, who was not injected, watches on he asks his former colleague "What did you do?" for which Kun replies "I gave them the knowledge I promised."
As the attack on Coruscant continues, Ulic Qel-Droma lands and makes his way to the war room. Mandalore's men strike and take new weapons while Aleema gives the command to her people to pull back when called upon. The Jedi manage to escort Master Vodo to the war room as he has requested , sensing Ulic will be there and it will be where the battle is to be decided. As Ulic is confronted by his old friends, Aleema tells her people to retreat and informs Mandalore that Qel-Droma is dead. Ulic now finds himself betrayed by his lover and left in the hands of the Jedi. Ulic's remaining soldiers are disarmed by the Jedi while Nomi and Master Vodo use the "Jedi blocking" technique which renders Ulic powerless. Ulic is then told by the council of Coruscant that he will stand trial and be sentenced to death...
Meanwhile on Yavin Four, Exar Kun prepares his new dark Jedi for an attack. "We must show the entire Republic and all of the other Jedi - never to underestimate the power of the Sith."
On his home planet of Dantooine, Master Vodo-Siosk Baas continues to blame himself for Exar Kun's downfall. He decides he must intervene at the forthcoming trial of Ulic Qel-Droma, as he believes the young Jedi is just a victim, and that the real enemy is his former apprentice.
On Cinnagar, in the Empress Teta System, Lady Aleema is moving on without her lover, Ulic Qel-Droma, as the new ruler of the Krath and executing anyone who objects to her ways. Her war advisor, Mandalore, suspects that Ulic was betrayed and plans to rescue his master after their attack on Kemplex Nine - a Republican shipyard.
Meanwhile, on Coruscant, Cay Qel-Droma and Nomi Sunrider rush to the commencement of the trial of Ulic. As Ulic is ushered into the court room he vows he will not repent.
Exar Kun's newly acquired dark Jedi have returned to Yavin Four after acquiring their own ships. Now Kun has new orders for them - they are to go to their old Jedi Masters and destroy them. "Before we can proceed to our golden age, we must remove the foundations". As Kun's new apprentices head off on their assignments, an unexpected ship arrives to greet the dark Jedi Master. Mandalore steps out and asks for Kun's assistance in the rescue of Ulic for which he accepts and together they head off for Coruscant.
After arriving they proceed to the hearing where Ulic is being branded a criminal by the council with only his brother Cay trying to defend him. Kun puts a Sith spell on the entire assembly of the Republic and kills the head judge. Ulic tells his brother that he can either join him or leave him alone, "You'll have to kill me if you want to stop me". As they prepare to leave they are interupted by Master Vodo who confronts his former apprentice, Exar Kun, and they duel. Kun urges his master to join him but Vodo will not have anything to do with it. In the end, Vodo is destroyed but vows that they will fight again, and next time he will win.
Kun and his loyal servants leave while Nomi and Cay comfort Sylvar, who mourns at the death of her master. Kun: "we are tired of serving their weakness, and we will work toward our own ends from now on. The Sith brotherhood controls the galaxy."
Nomi Sunrider, her daughter Vima, and Sylvar (Master Vodo's apprentice) are greeted by Jedi Master Thon as they arrive on Ambria for a time of quiet healing. Little do they know that overlooking Thon's home are Oss Wilum and Crado, both of whom have been sent by Exar Kun to kill Master Thon.
Using his Sith powers, Oss Wilum releases the dark side creatures that Thon had confined to the lake, and sends them to attack Wilum's former master. The Jedi, however, easily defeat the creatures and while Sylvar fights her old lover Crado, Thon is dismayed to capture his own student, Oss Wilum. Sylvar lashes out at her fellow Cathar and calls him a traitor, Crado retreats to his ship, comforting his wounds. As Thon returns to his home with his Jedi and the fallen Wilum, his concerns flow out to the other Jedi Masters throughout the galaxy.
They are not as safe, as many of Exar Kun's possessed apprentices seek out their masters and destroy them. Jedi knights Dace Diath, Shoaneb Culu and Qrrrl Toq arrive at the afterpath of a battle between Master Dominus and his ex-student Zona Luka both of whom were killed, sadly it is not the only remains of Jedi Masters they have found recently.
On Yavin Four, Crado returns from his failed mission and reports apologetically to Exar Kun. Crado vows to make it up to him and requests to be a part of the mission to Kemplex Nine. Kun agrees for him to be the battle commander for Aleema - who is leading the attack along with carrying an ancient Sith weapon on board. Mandalore is confused as to why he was not selected for the position and why Ulic chose Aleema to lead the attack after she betrayed him.
On Ossus, Jedi knights Dace Diath, Nomi Sunrider, Qrrrl Toq, Cay Qel-Droma, Shoaneb Culu and Sylvar, along with Jedi Master Thon, meet together in a time of grief and betrayal. Thon warns them to put their feelings aside as this is a war between light and darkness. Suddenly Tott Doneeta enters the meeting and informs of an attack at Kemplex Nine. Thon remains skeptical - "I Fear this attack is a feint. What could they want at Kemplex Nine?" while Dace Diath, Shoaneb Culu and Qrrrl Toq volunteer to join the counterattack.
Kemplex Nine, a space station, lies in a hot, unstable cluster of ten stars known as the Cron Cluster. The three Jedi knights arrive in this area in hot pursuit of Aleema's warship. Using the ancient Sith weapon aboard, Aleema rips the core from the center of one of the stars causing a huge explosion which innolates the three Jedi knights and the Republican ships. The blast does not stop however, as it continues to destroy star upon star within the system and destroys everything in its way, including Aleema and Crado, who realise too late that they have been betrayed by Ulic Qel-Droma and Exar Kun.
On Yavin Four, Kun and Qel-Droma discover all is proceeding to schedule and that the immense inferno is headed directly for Ossus. Kun plans to travel to Ossus and raid the great library while its inhabitants retreat to safety.
The deadly shockwave continues its destructive path towards the planet Ossus. While the inhabitants plan their evacuation, Ulic Qel-Droma and Exar Kun are just arriving. Their mission - to claim Jedi artifacts for themselves. At the great Jedi library Jedi knights Cay Qel-Droma, Nomi Sunrider, Tott Doneeta and Master Thon are assisting with the preparations. Cay senses his brother's presence and quickly rushes to his own ship, the Nebulon Ranger, to follow him.
Meanwhile, Exar Kun lands his ship, the Starstorm One, and with a squadron of Massassi head into a private alcove of the library where Master Ood is collecting ancient lightsabers for the evacuation. Knowing he cannot defeat Kun in combat, Master Ood decides to sacrifice his life to protect the artifacts by using the force to turn him into a powerful tree which is inpenetrable to any strike. Kun, though disappointed, decides his other Massassi have collected enough artifacts for them to now leave but not if Jedi Sylvar has anything to do with it. After attacking several Massassi, the Cathar turns her focus on her old colleague, Exar Kun, but he has no time for her and returns to his ship while several of Kun's warriors knock her out.
Elsewhere, Tott Doneeta, Nomi Sunrider and Master Thon notice among the scavenger ships that two of the crafts are those of the Qel-Droma brothers. Nomi and Doneeta run towards them as Ulic's ship strikes at the Nebulon Ranger bringing it down. Cay manages to escape his destroyed ship to find his brother, Ulic, waiting for him with a lightsaber raised. Cay, unwilling, raises his own lightsaber and the two battle it out. Cay attempts to convince Ulic to turn to the light, to drive the Sith poison and the dark side out of him but Ulic is outraged, he wants to be left alone by his brother and his lightsaber takes care of that - Cay Qel-Droma is killed. Nomi and Tott Doneeta arrive but it is too late, Ulic in the meantime realises what he has just done and falls to his deceased brother, holding him tightly.
Nomi Sunrider is so horrified to find her former lover has killed her friend and his own brother that she uses the force to imprison Ulic Qel-Droma in a wall of light and in doing so renders his Jedi powers useless. Ulic is terrified to find his powers are gone and that he is no longer a Jedi. On Onderon, Mandalore continues out his orders of attacking the home planet of Freedon Nadd to claim for his masters but Oron Kira and his forces are ready for such an attack, as his beast-riders prepare to defend themselves.
Meanwhile on Ossus, Nomi Sunrider contemplates what she has done to Ulic Qel-Droma while Ulic himself is comforted by Oss Wilum (having had the Sith poison driven out of him) who asks his help in stopping Exar Kun. Ulic reveals the whereabouts to be Yavin Four and the Jedi plan to form a rally to confront their enemy but first they must leave this doomed planet. Master Thon, however, has to do one final thing - visit an old friend, Master Ood. Ood tells him not to grieve for his fellow friend and colleague, that he is satisfied that he defeated Exar Kun from removing the artifacts and that who knows, maybe the planet's core will protect him. The remaining inhabitants on Ossus evacuate the place, Ulic carrying his brother Cay, as they leave just in time before the shockwave, the explosion of ten suns, sears the face of Ossus.
On Onderon, as the battle continues, Oron Kira receives a pleasant surprise - the Republican reinforcements arrive. Mandalore's fleet is slowly destroyed and he and the final survivors of his squadron flee to the Dxun moon. Heavily pursued by the Republican fighters and Kira's war-beasts, Mandalore's ship is struck and he ejects into the forests of the moon. Believing he has reached safety, he is quickly surrounded by the untamed native beasts and the rest is left for our imaginations to behold
In the Yavin system thousands upon thousands of Jedi knights arrive with the intent of defeating Exar Kun. Kun, watching from the moon Yavin Four realises he has been betrayed by Ulic Qel-Droma. Knowing he cannot defeat the combined might of the Jedi, Kun uses the powerful transformation weapon of Naga Sadow to transform him into a powerful spirit that will run rampant through the cosmos. Sacrificing thousands of Massassi, Kun's mortal body disinegrates and leaves the moon of Yavin Four in flames but not all has gone to plan for Kun. due to the Jedi knights unleashing a powerful wall of light. Sensing it is over, the Jedi ships depart Yavin Four and begin their attempts at restoring the galaxy and rebuilding the Republic.
On the Dxun moon, surviving Mandalorian warriors search for their master only to find his helmet. The warrior who finds it places it on his head and says "Now I am the new Mandalore", the tradition continues
Two years later, Ulic Qel-Droma arrives on Yavin Four looking for any remnants of Kun, finding nothing he leaves in his ship, named "Cay's Dream". Leaving a trapped Exar Kun behind