Jedi Andur Sunrider, his wife Nomi, and their child Vima, venture to the Stenness System to find Jedi Master Thon and thus complete Andur's training. However, when stopping at a mining station, henchmen to a mighty Hutt named Bogga learn that Andur is carrying Adegan crystals (used to make lightsabers), and attack him. Andur is killed while Nomi, in a fit of rage, uses her husband's lightsaber on the attackers, she kills two of three. A vision of her husband tells her to continue on the journey and find Master Thon.
Nomi, accompanied by her infant daughter and droid (A-3DO), journey to the planet Ambria in search of Master Thon. Along with her daughter, Nomi travels across the vast desert lands of the planet, which seem to be strong with the dark side, until she meets a jedi named Oss Wilum and his bestial companion.
Meanwhile, greedy for the Adegan crystals Nomi has in her possession, Bogga the Hutt has followed the young woman to Ambria and after damaging A-3DO, tracks her down to her current location. Oss Wilum defends his home and is nearly killed until his companion defeats the attackers with an amazing amount of power in the force, forcing Bogga and his men to flee. Nomi then learns that the beast is actually Master Thon.
Months have past since Bogga has attacked and Master Thon was revealed. Nomi Sunrider has basically been ignored during this time by the Jedi Master who considers her to be in a time of mourning. While pondering over Thon's strange behavior, her daughter Vima wanders off into trouble as she nears the lake where dark side dragons dwell. As the dragons move to attack, Nomi, using a unique talent of meditation, forces them into attacking each other. As she grabs her daughter and pulls her to safety, Nomi begins to wonder why she couldn't have used this power of hers to save Andur. She remembers the times when her husband was in training to be a Jedi and wishes he still lived. Vima asks her mother if her father will be coming back for which Nomi replies "I Wish...it was true, Vima. I Don't think we'll be seeing him again." As they return to their camp, Master Thon decides it is time for her Nomi's training to begin.
Meanwhile, in the Stenness Node (a group of mining systems on the galactic frontier), a cargo ship transporting Mutonium ore to the Stenness Hyperspace Terminal, is attacked by pirates who attach their ships to the hull and begin stealing the valuable ores. The Captain of the cargo ship, Gruna, questions the location of his expensive escort, supplied by Bogga the Hutt, as his ship stands defenseless. It is not too long however, that Bogga's ships appear. Striking the ore pirates' ships and using the Hutt's massive dreadnought's tractor beam they capture the pirates. As the leader of the pirates, Captain Finhead Stonebone is taken to Bogga, he claims he did not know he was trespassing on Hutt territory, though this of course is a lie.
Back on Ambria, Oss Wilum is repairing A-3DO when Nima asks him why Master Thon chose to live on this remote planet. Wilum tells her that Thon did so to "test himself, for Ambria is a dark side world, and once he drove back the dark side energies back into the wilderness, he decided to stay." Nomi feels relaxed that Oss Wilum is here to talk to, (she finds Thon a little scary at times) but Wilum informs her that a jedi named Tott Doneeta, a Twi'lek, has arrived from the other side of the galaxy to get his help in fighting against the Freedon Nadd Uprising.
Master Thon approves Oss Wilum's departure and together with Tott Donetta, he heads off towards Onderon while Nomi, he daughter Vima and Thon farewell them (ohh, A-3DO is there as well).
On Bogga the Hutt's private moon, the mighty dreadnought lands with its captives - the ore pirates, led by Finhead Stonebone. As Stonebone is placed in front of Bogga's throne, the hutt tells him he would normally die for his acts but Bogga (also known as "The Merciful One") is giving him an alternative to dying which involves the Hutt's new enemy - Master Thon.
On Ambria, Master Thon begins his training with Nomi Sunrider. Nomi, who realises that she can understand him even when he speaks in beast tongue, tells Thon that she knows she must become a Jedi but she will never use a lightsaber again. Thon, however, believes in another destiny for his new apprentice but doesn't bother to pursue this matter at the time and takes Nomi and Vima outside where he will give them a ride up to the hills. Nomi though, is still unsure of her new Jedi Master and a little worried.
On the moon of Taboon, Captain Finhead Stonebone refuses Bogga's demand to kill Jedi Master Thon and return the adegan crystals. Bogga then offers incentive by sacrificing Finhead's first mate, Roko, to Bogga's ferocious beast, Ktriss. As Finhead watches his friend being devoured by the creature, he realises he has no choice but to obey.
Due to the gentle art of persuasion, Bogga the Hutt has convinced Captain Finhead Stonebone that he is to travel to Ambria where he will kill Master Thon and steal the adegan crystals.
On Ambria, Thon continues to train Nomi Sunrider. As he takes her through the countryside of his planet he tells her that the lightsaber is not only a weapon of self defense but also a tool for meditation for which she is to create one using the adegan crystals. Nomi, however, declines the offer, refusing to have anything to do with lightsabers. Master Thon doesn't pursue the matter for the time being and goes on to show her a Jedi holocron where a Jedi Master named Ood Bnar tells her of the ancient times when the Jedi Knights fought against the armies of the dark side. Ood Bnar then tells them that a great struggle is coming, that the dark side will rise and that many great Jedi knights will fall to its seduction. As he looks at Nomi, Bnar points to her and says that she will play an important part in the battle and that she will be strong.
Once again Master Thon instructs her to take up the lightsaber and this time he gives her his own. As Nomi takes it she decides to herself that she will leave this planet, and her new master, to start a new life. Thon, however, can sense her feelings and warns her there in no going back for her now; "There is going forward ... or there is darkness".
As Nomi struggles to come to terms with her involvement in a foretold galactic battle, Stonebone's men and Bogga's enforcers land on Ambria. They attack Thon's hut only to find A-3DO there, but soon enough Thon and Nomi come into sight. As Thon uses the force to deflect their blasts he urges Nomi to take up the lightsaber but once again she cannot. Finally they come into direct aim of the pirates and enforcers, Thon tells Nomi that if she will not use her lightsaber then she must use her meditation powers. Nomi, however, is naive of these powers and instead decides to dismount Thon and take Vima to safety.
While Nomi hides Vima behind a rock where A-3DO awaits, Thon surrenders without a fight. Feeling remorse, Nomi knows she must do something. Eventually realising her unique mental ability she turns Finhead's and Bogga's men against each other. To save Thon from the attackers though will require some other force, that of a lightsaber. She hesitates at first but as she ignites the lightsaber the horrors of doing so disappear and heroic traits of the future emerge. She defends her master, as he had hoped, and her fears of this Jedi weapon have diminished. Thon, together with his apprentice, manage to defeat their enemy - many of whom flee back to their ships - including Finhead Stonebone - and escape.
That evening the relationship between Master Thon and his greatest apprentice, Nomi Sunrider, is a lot less tense. Thon tells her that she will be a great Jedi but Nomi knows that times forthcoming will not be easy .