Following the end of the Beast Wars, the new Onderonian monarchy and their Jedi allies led by Master Arca Jeth make preparations to transport the sarcophagi of the dark siders. Jeth is assisted by his apprentices Ulic Qel-Droma, Cay Qel-Droma, Tott Doneeta and Master Thon's apprentice Oss Wilum. The new Onderonian Queen Galia and her husband Oron Kira want to purge Iziz of Nadd and Amanoa's dark side influence. The Onderonian military has prepared a tomb on the moon of Dxun for Nadd and Amanoa.
Before they can load the remains of Nadd and Amanoa aboard a starship, a groundborer digs through the surface of the spaceport and dispatches several hundred Naddists, led by Warb Null. While distracting the Jedi and Iziz forces, a group of Naddists are able to snatch the sarcophagi and take it back with them underground into the sub-levels of the kilometers of the deep city.
Master Arca senses a dark side influence from the depths of Iziz. Queen Galia suggests that her father King Ommin, who has been confined to a life-support facility for many years, can help. While Cay, Tott and Oss Wilum secure the royal palace, Master Arca and Ulic travel with Galia to Ommin's facility. Arca demands to know the location of Freedon Nadd's sarcophagus but a defiant Ommin reveals that Freedon Nadd is among them.
The Force ghost of Freedon Nadd soon manifests and Master Arca realizes that he is the source of the dark side influence in Iziz. Empowered by the spirit of Freedon Nadd, Ommin betrays his seemingly immobile state by attacking Master Arca, knocking him unconscious. Warb Null comes in and attacks Ulic, but is soon bested and killed by the young Jedi. Unfortunately, this gives Ommin the time he needs to kidnap Master Arca.
Ulic and Galia return to the royal palace only to find that it has been captured by the Naddists. They meet up with Cay, Wilum, and King Oron and escape on Drexls to Modon Kira's fortress in the wilds to regroup. Tott also transports the Beast Riders to Kira's citadel. Realizing that they are outmatched by the dark side, Ulic decides to call for Republic and Jedi reinforcements.
Meanwhile, Jedi Master Thon arrives on the planet Ossus with his new apprentice Nomi Sunrider and her daughter Vima Sunrider. Ossus has been a Jedi center of learning since ancient times. Master Thon introduces Nomi and Vima to Master Vodo-Siosk Baas, who is teaching Dace Diath how to build a lightsaber. While Thon takes Vima to play with some Jedi children, Vodo introduces Nomi to another Jedi student named Shoaneb Culu, who is also learning how to build a lightsaber.
After a week of instruction, Nomi builds a green lightsaber. After several weeks of training, Nomi and several Jedi volunteer to rescue Master Arca from the Naddists on Onderon. Nomi and four other volunteers Dace Diath, Shoaneb Culu, Kith Kark and Qrrrl Toq are chosen fir the mission. While Vima is safe with the other Jedi children on Onderon, Nomi and her comrades travel to Onderon to participate in the forthcoming Second Battle of Onderon.
On the galactic capital Coruscant, the Defense Minister and several senators debate about sending military forces to assist Ulic on Onderon. Meanwhile, heirs to the Empress Teta system royalty and members of the Dark Side cult the Krath, Satal and his cousin Aleema Keto, visit the Galactic Museum and find a fascinating Sith book.
Satal steals it while the curator isn't looking and return to their lodgings. Satal and Aleema are unable to read it. After seeing a news report about the Sith practitioners still active in Iziz, the Ketos fly to Onderon to find said practitioners and discover the secrets of their new book.
Exiting hyperspace, they find Onderon blockaded by the Republic Navy, which has imposed a security military zone. Defying the Republic blockade, the reckless Satal flies the Tetan Royal Space Yacht Krath Enchanter through the Republic ships. When Aleema asks if he is going to get them killed, Satal responds that he is not letting the Republic get to the Sith magicians before they do.
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