Two new students, Wilcra Li New and Meja Codan, arrive on Yavin IV to begin their Jedi training. They are met by Jedi Knight Ash Tor, who takes them on a tour of the temple, the location of Luke Skywalker's Jedi Academy.

After their tour around the Academy, Ash Tor takes Wilcra Li New and Meja Codan to the top of the Massassi temple where they meet Master Skywalker himself, and two other new students called Yazh Ghyron and Macan Vesso. Luke tells them that another Jedi named Kyle Katarn will start their training, and when they are accomplished enough they will be assigned their own personal mentors. They meet Kyle who tells them to get to know each other and settle in, as their training will begin first thing the next morning. They talk a little bit so we learn where they're all from. Ghyron's and Codan's overconfident personalities immediately start to conflict.

Codan has piloting experience. Ghyron thinks becoming a Jedi will be dead easy. Macan was a hyperdrive mechanic on Ord Mantell. Li New was raised hearing stories about the Jedi in the olden days and has learned to respect them.

In the training areas of the Academy, Kyle starts to put the new recruits through their Force training. They are also given their first sabers and do some remote training. They use the metal-bar-in-the-air trick, that Luke was supposed to do in Empire Strikes Back.

Macan is in the hangar where a Rodian Jedi, named Reeldo, and some droids are trying to fix a ship and he helps out. He gets his first glimpse of a woman named Peta, and is instantly entranced. Ghyron notices his look and annoys Macan, telling him to get in line because he saw her first.

Peta and Macan meet, and she thanks him for helping her master, who had been trying to get rid of the intermittent problem with his ship for weeks.

A run through an assault course sees Macan and Li New competing against Ghyron and Codan. Kyle wants to see if Li New can put some confidence into Macan, if Macan can get more confident, and if Ghyron and Codan can start working together. Codan and Ghyron race off into the lead but their desire to beat each other gets in the way and they end up allowing Li New and Macan to finish before them. They argue a little bit, each blaming the other.

Ghyron tries to talk one of them into a practice saber duel. Despite Li New and Macan trying to persuade Codan to ignore him, Codan wants to prove a point and accepts. Ghyron shows little respect for Codan's life, and Kyle comes in to break it up and warn them both.

The students are sent with Kyle Katarn on their first mission. Kyle calls it a "blue milk run", assuming it will be an easy mission, as it involves mediating between two groups. Unknown to the Jedi, some of the people involved are Imperial Remnant who are working for a Dark Jedi named Andeur Drakesh. When Drakesh finds out Jedi mediators are involved, he orders an ambush which separates Kyle and Li New from the other students, and a fight ensues.
Things escalate rapidly, as the students are forced into real action for the first time, and they defend themselves from blaster fire. Codan and Ghyron clash again over whether to play it safe or go on the offensive, and during their squabbling Codan gets shot in the leg and they both get captured, as Macan is forced to flee.

Kyle and Li New meet up with Macan, and together they are able to rescue Codan and Ghyron before Drakesh can get to them. The Remnant's influence on the planet is rooted out, and all is eventually set right.

When the Jedi return to Yavin, Kyle and Luke discuss the proceedings, as Codan and Ghyron's hatred for each other continues to grow.

On a desert planet in the Unknown Regions called Terrinak, a mysterious, cloaked humanoid is stood beside a member of the indigenous insectoid species called the Garron-Hinn, as the Hinn itself is accepted as the species' new leader.

Two years later, chaos ensues on and around a space station orbiting the planet Reejan. An A-Wing starfighter appears out of hyperspace and races towards the battle. The fighter is flown by Peta, and she takes out enemy fighters by the bucket load before strafing the station, bringing down its shields. She then leads a landing party onto the station.

Meanwhile, already on the station, Macan is running and dodging down corridors, trying his best to protect a legislator, Narmay, who he was assigned to guard. Hot on their heels is a group of elite bounty hunters who have been offered a small fortune in credits to kill said legislator.

As Macan is finally cornered, Peta arrives just in time to help. She wades into the bounty hunters from behind as Macan desperately deflects a volley of fire.

Peta learns from Macan and Narmay that Reejan has a massive problem with black markets and smuggling, and Narmay has been the foremost polititian trying to do something about it. Narmay was on the station for security talks, which were supposed to be secret, and now believes there are spies in the government.

After clearing up the remaining aggressive ships and combatants on the station, Codan and Ghyron join them. After contacting Kyle and Luke, Codan and Ghyron are given the task of rooting out the corruption, now that they appear to be working together a little better, while Peta and Macan are asked to return to the Academy.

On the planet Reejan, the goverment is run by the Sydor family. The governor, Vilton, is unwell, and is preparing to pass the reigns down to his son, Airon. This development has pissed off his daughter, Airine Ellin, and the two Jedi later discover it is she who has been feeding confidential intelligence to an enigmatic underworld group called the Guild Of Zevuras, who work in the shadows to influence and disrupt things that happen on the planet. As part of this group, she is known as Lady Diarrus.

Back at the Academy, Macan checks Peta's fighter wasn't too damaged, and the attraction between the two is obvious. Macan later meets Li New, who is studying ancient history. Li New voices his concern that Macan's fascination with Peta is hampering is learning, and he wants Macan to do well in his efforts to become a Jedi, as so far, he is the only one of his fellow students that Li New really trusts.

On the trail of Lady Diarrus, Ghyron is approached by someone calling himself Vorasus, another member of the Guild, who reveals himself to be Force sensitive, before offering Ghyron a choice.

The Jedi eventually find where the next Guild meeting will take place, and they crash the proceedings along with the authorities. The Guild members scramble to escape, though some of them open fire with concealed weapons. When Vorasus pulls a gun, Ghyron Force throws a chair at him, smashing him through a nearby window and sending him hurtling to his certain death many stories below.

Several members of the Guild are killed in the ruckus, and most of the others are apprehended. The leader of the Guild, the one who called himself Zevuras, is found dead, stabbed by a strange knife that is not found. It turns out that Zevuras was really Fodor Lacki, the director of the Zenor Company, one of the largest organisations on the planet, who deal in the trading and manufacturing of many technological items.

As the cleanup continues, Codan finds he is unable to locate Ghyron, and he is left to help the government handle the fallout and revelations of the Guild's existence on his own.

In a dark hangar somewhere, Ghyron walks up the ramp of a small transport ship. Its door slides open, and he is greeted by Vorasus. He enters the ship and they leave the planet.

On Yavin, Peta is promoted to a Jedi Knight. She and Macan discuss their future, and decide that they will be together once their training is far behind them and they are both more capable of handling their skills and emotions in a mature way.

A year later, there is still no trace of Ghyron. Li New is the only Jedi still actively searching for him. Codan wants to help, but Kyle wants him to meditate and study some more. Codan gets a bit pissy when Kyle compares him to Ghyron in that they both have a lust for action. They also speak about how Macan's training has been coming along at a much faster pace. Codan thinks it's because Peta has been supporting him. He worries that Macan only believes in himself because Peta does, and he doubts Macan has really found his own self confidence yet.

On Reejan, Airon is to become the new governor, and after his sister is sprung from prison, Peta is sent to protect him in case any trouble goes down. Her presence is soon discovered by a group of Dark Jedi, who are responsible for Airine Ellin's escape. The leader of the Dark Jedi, a mysterious man in a hooded cloak, orders two of his newest recruits, a young man named Kreygor, as well as Ghyron, to kill the Jedi, while he observes with several other Dark Jedi.

Peta, on the trail of whoever sprang Airine Ellin, is attacked by the the Dark Jedi on a bridge spanning two high-rise buildings, while the other Dark Jedi observe from a balcony higher up. During the duel, Peta catches a glimpse of the onlookers, and does not recognize the species of one of them, as it is the Garron-Hinn individual.

The far too overconfident and brash Dark Jedi are initially taken to the cleaners by the calm and precise skill of Peta, and after a few moments she manages to sever Ghyron's right arm at the shoulder. As he screams in pain, Peta takes him down by hacking off his right leg half way down his thigh. Realising he has underestimated his enemy, Kreygor then takes the fight to Peta with more anger and determination than before, and he puts Peta on the back foot.

At the Academy, Macan is suddenly overcome by a chilling sensation through the Force. He assumes the worst, and gets angry and emotional at Master Skywalker for sending Peta to Reejan alone. Luke heads off to Reejan with a small group of other Jedi.

With the duel over, Kreygor simply turns and begins to walk away, leaving his opponent's lifeless body in a slump. Ghyron, roaring with anger and pain, pleads with Kreygor not to leave him. Kreygor wonders why he should care about someone so weak, but Ghyron promises him that he will have revenge on the Jedi for what they have done to him. The cloaked figure indicates he wishes Ghyron to be retrieved, so Kreygor does as he is instructed.

Later, Luke returns to the Academy, and breaks the sad news to Macan. Macan explains his regret for how he spoke to Luke earlier, but finds he can no longer continue to train as a Jedi. With sorrow, Luke, Li New and Codan watch as Macan leaves on a shuttle.

In a dark and mysterious medical room, Ghyron lies on an operating table, painfully receiving cybernetic limbs, as Kreygor and the Garron-Hinn look on with the cloaked figure.

Soon after, another Jedi student called Ja'nalora is promoted to Jedi Knight, just before it is discovered that her younger sister, Karynna, who is also a Jedi student, has gone missing.

Two years later, Li New and Codan are promoted to Jedi Knights after foiling a Dark Jedi plot to kidnap and control a group of scientists.

As a proponent of the Master-Padawan dynamic, Li New immediately takes a student named San Rylo.