One year after the events of The Dark Side Of Do'Naar, it is night time on Tatooine. Someone runs panicked. Two cloaked figures stride after him. They go through the streets of Mos Espa, until they come to a place where a few vicious looking brutes and droids emerge. Someone up on a roof shouts a warning down to them, stating that they shouldn't be chasing their friend. The mob sets about the two people. The two figures cast aside their robes and we see they are Jedi: Codan and Macan. Their sabers ignite as their target flees. The Jedi disable the group, then chase the man down and detain him.

All along it seems they have been after information about Dark Jedi whereabouts. They had recently overheard in one of the bars that this person had boasted he had intercepted a transmission by the Dark Jedi and had managed to escape them as they sent assassins after him. The man tries to claim that the Jedi are mistaken but he eventually gives in. He tells them about where he was: the Raddus system. At first the Jedi think it has all been a waste of time, as they already know the Dark Jedi had been to Raddus, but the person lets them listen to a recording of the transmission. Codan recognises a voice as Akkam Songar, and realises he was lied to. The Jedi head back to their ships and open a transmission to the Academy. They talk to another Jedi called Ja'nalora, and we learn that a lot of the Jedi are searching for clues of Dark Jedi whereabouts.

Ja'nalora is especially interested as we learn that she is still searching for her sister Karynna, who they now know is a Dark Jedi who was encountered on Do'Naar. Codan and Macan say they will meet Ja'nalora at the Raddus system in a couple of days, then ask if there is any word yet from Li New and Rylo. Ja'nalora says no, but informs them Luke has not yet sensed any danger or failure from them.

Elsewhere in the galaxy, a group of pirates & smugglers are doing some dodgy missions for the Dark Jedi. The smugglers are just about to go through with the first part of a big operation. We see that two of the smugglers are actually Li New and Rylo, who have managed to infiltrate them.

A day or two later the first part of the smuggler mission is a success, mainly thanks to Li New and Rylo, further helping the smugglers to trust them. The lead smuggler receives orders about where to make the delivery, and they head off.

Codan, Macan, Ja'nalora and her Padawan Shanna are on Raddus-Bor. They are hunting for Akkam. Eventually they find him under attack from a mercenary, and they fight off his assailant. Ja'nalora and Codan force him to talk and he explains his involvement with the Dark Jedi. How the Master hired him to spy on Kreygor, and taught him how to mask his feelings from the Force. But now the facility is gone he is no longer needed and the Master has been trying to kill him. He says he does not know who the Master is but the communications came from the planet Reejan. Codan and Macan throw each other a glance. The planet's governor was supposed to be on the look out for Dark Jedi and inform the Jedi if any turned up. The Jedi still have their lead, and head off.

The smugglers arrive at the planet Reejan with their bounty, and meet up with the Dark Jedi envoy: Ghyron, Karynna and Drakesh. Li New and Rylo try to stay hidden but the lead smuggler gives them so much credit and builds them up that the Dark Jedi ask them to step forward. It is immediately obvious their disguise is not good enough. Ghyron recognises them and immediately tries to kill them. Li New and Rylo flee the area as Ghyron explains. Drakesh orders Ghyron and Karynna to kill the Jedi and they head off. Drakesh is not happy with the smuggler leader, and drags him away.

Li New and Rylo have stolen some speeder bikes and they race through the city as Ghyron and Karynna chase them on their own speeder bikes, guns blazing. After a hectic chase the Jedi lose their pursuers who fly away.

Drakesh throws the lead smuggler at the feet of the cloaked figure and another Dark Jedi, the white-skinned Ashaai, Meiden. Drakesh explains what has happened and the Master frazzles the lead smuggler with lightning for being foolish and careless. Meiden asks if killing him was necessary, but the Master tells his followers that Reejan's usefulness has run its course and it's time to move on. He orders Ghyron and Karynna to load up the smuggler's equipment and evacuate, and tells the smugglers if he ever sees them again he will kill them like he did their boss. They are not happy about not being paid as the Dark Jedi leave.

Codan, Macan, Ja'nalora and Shanna arrive at Reejan and through the Force learn of Li New and Rylo's presence. They all meet up and discuss the goings on and decide on what action to take. Li New and Rylo didn't have their sabers because of their disguise. So they head off to inform the authorities/governor while the other 4 Jedi move to intercept the Dark Jedi and smugglers.

The smugglers talk as Ghyron and Karynna are loading their starship with the supplies. They decide that they can't let the Dark Jedi get away without paying them something, as they have done a lot of work for them.

Li New and Rylo are within the governors palace, and explain about the situation. He is shocked and apologises but assures them he had no idea what was going on. The governor sends a military squad under the command of the Jedi to help sort out the mess, while he tries to figure out how the Dark Jedi have continued to operate undetected.

In the starport, the smugglers get their weapons from their ships and confront Ghyron and Karynna. They demand that they be paid. The Dark Jedi warn them to back down or they will die. The smugglers don't and the fight kicks off. Just then, the Jedi arrive and observe the scene.

The Jedi are pulled into the explosive 3-way battle. The heavy weapons of the smugglers prove to be a handful even for the Jedi and Dark Jedi, and some of them get into their ships and open fire with the craft's weapons. The starport is rapidly going up in flames as the fight rages.

Li New and Rylo arrive with the planet's soldiers, and the Dark Jedi flee as the smugglers begin to be overwhelmed. Codan and Ja'nalora follow them into the next hangar.

Codan and Ja'nalora fight Ghyron and Karynna. The battle goes on for a while until Ghyron takes off and hassles Codan from the air. The Jedi is lured away as the two sisters go at it. Though Ja'nalora beats Karynna, and tries to talk her round, Karynna just laughs her off. Ja'nalora finds she can not kill her sister. Karynna though has no problem and slides her blade through her opponent when she's off guard. Codan realises he has been tricked and rushes to Ja'nalora's side but it is too late. Ghyron, finding it all quite amusing, lands beside Karynna and Codan comes under attack from both Dark Jedi.

In the other hangar, the smugglers and their ships are still proving problematic. Shanna saves Rylo, reminding Macan of when Peta saved him. The Jedi then kick things up a notch and Macan's new skills and confidence are evident as he helps subdue the remaining smugglers.

Macan and Shanna quickly rush to help Codan as he comes under attack. Ghyron and Karynna again flee, and due to Ja'nalora's demise the Jedi do not follow.

The planet's authorities clean up the smugglers. The governor indeed learns that someone in his team was again working with the Dark Jedi.

Codan is distraught at the realisation of what he has done. He talks to Li New about how bad he feels about Ja'nalora. He starts to doubt his mentality as a Jedi, how he let his feud with Ghyron blind him from the bigger picture.

While this is going on, Macan feels drawn by something. He finds himself led across the city to the spot where Peta was killed. There, he meets her Force ghost and they talk. She is proud of how far he has come, and he begins to understand that when she told him he would never be alone, she really meant his friends would be with him, and not her. Though she promises to watch over him always, she vanishes, and Macan realises that was the last time he will ever see her face.

Later at the Academy Codan is still heavily blaming himself for Ja'nalora's death, and Li New offers his support.

Luke, after hearing the reports and talking to Macan, decides Macan is ready. Li New explains he also has confidence in Macan, and Macan remembers Peta's words about friendship. Macan is promoted to Knight.

Later Luke talks to Codan, trying to reassure him. He thinks Codan will be a good choice to continue Shanna's training, and explains that Macan has become a Knight. Codan is still very unsure, but Luke assures him he will learn from this and become an even better Jedi.

Shanna herself, after learning of Luke's suggestion, goes to Codan and explains she still has the utmost confidence in him, and would be proud to have him help her finish her training. Codan is still unsure, and as he faces the decision of what to do next, the Jedi meet a worried looking Kyle Katarn. Katarn has just received word that a new enemy from beyond the galaxy is invading, and that Chewbacca is dead and the planet Dubrillion is currently under seige. The Dark Jedi are suddenly the least of their worries as they realise the galaxy at large is now at war.

After the five-year long war against the Yuuzhan Vong is over, the galaxy and the Jedi have changed. San Rylo and Shanna were promoted to Knights part way through the war along with other Jedi students. With the loss of the Academy during the war, the Jedi trio and their allies now reside on the Dawn Of Peace carrier.

A blossoming romance between Rylo and Shanna gives Li New some issues, and he and Rylo have a heated discussion. Li New simply doesn't want what happened to Macan to happen to Rylo, but the younger man wants his former Master to mind his own business.

Learning of the tension, Mara Jade approaches Li New and they discuss Rylo's situation. She tries to get him to see how much inner strength love can give a Jedi, like it does for her and Luke, and that baby Ben wouldn't exist without it.

Knowing the Jedi have been weakened after the war with the Vong, the Dark Jedi want to press their advantage. The Garron-Hinn Dark Jedi, which they call the Garsanekra, is unleashed for the first time, where it duels with Master Reeldo and Ash Tor. Reeldo is killed and Ash Tor badly injured before the latter manages to escape.

On their search for clues about this new threat, the Jedi find a Star Destroyer, badly damaged by the Vong. After clearing out an aggressive group of scavengers, Li New has an idea about what to do with it.

By sheer luck, or the will of the Force, Macan recognises Karynna when out on a fairly unimportant mission. Realising that she has not noticed him, he is able to place a tracker on her ship. He is able to follow her into the unknown regions, to a planet called Terrinak. Beneath the planet's barren and desert surface, he finds a catacomb of tunnels and chambers belonging to a large insectoid species called the Garron-Hinn. When he learns that the Dark Jedi are working with and arming the Garron-Hinn for war, Macan heads back to his ship to alert the Jedi. Before he can get there, his presence is discovered by the Garron-Hinn, and his ship is destroyed.

Figuring that Macan has followed Karynna, the Dark Jedi Master calmly executes the Twi'lek with her own saber.

Macan is then hunted through the caverns of Terrinak by the Garron-Hinn and Dark Jedi. He is first challanged by Raelag, and the two combatants fight with their duel-bladed lightsabers until Macan's is damaged. He ignites Peta's old saber and is able to defeat the evil Zabrak.
As he continues to flee, he is chased down by Drakesh and Meiden who are on swoop bikes. He is able to disable Drakesh's swoop, and the two Dark Jedi leap down to fight him. The battle rages through the tunnels until Macan is cornered in a cavern containing a large chasm. He kills Drakesh, but shortly after, Meiden displays astounding skills to disarm him.

Expecting death, Macan waits while the white skinned woman hovers her saber to his throat. As she hesitates, her Master appears and retrieves Macan's saber. Sensing the Jedi has an emotional attachment to the weapon, it gives him great pleasure to ignite it through the Jedi's chest. With a simple Force push, Macan's body is then sent tumbling into the chasm, after which the saber is also dismissed down into the abyss.
As Macan's body falls through the darkness, it vanishes, as he becomes one with the Force.

The Dark Jedi think they've prevented Macan from notifying the other Jedi, but while Luke is meditating, Macan's Force ghost appears to him and tells him everything he learned.

Luke prepares the Jedi and the New Republic for a large scale battle, but not before having a difficult conversation with Li New and Codan about what happened to Macan.

Republic and Jedi forces later arrive at Terrinak where they are met in battle by the Garron-Hinn's organic war machines, as well as Dark Jedi and other mercenaries hired by the dark side users.

The battle rages on, above and beneath the planet's surface. In the tunnels, Li New faces down Meiden, and learns that she is one of those responsible for Macan's death. In the middle of a large scale troop engagement on the surface, Codan faces Ghyron and finally strikes down his nemesis, despite the act requiring him to allow several nearby troopers to die.

As they hunt for the Dark Jedi Master, Luke and Mara Jade come face to face with the Garsanekra, who attacks them ferociously with four lightsabers. When Luke severs one of its limbs, it screeches in pain and retreats. They track it to a cavern where they discover the body of what is seemingly the Garron-Hinn's queen, which shows little sign of life. Nevertheless, they sense the Garsanekra's fear and anger, and it becomes obvious that it is willing to die to defend the queen. Luke and Mara try assuring it through the Force that they have no desire to hurt the queen, but the Garsanekra retorts, accusing them of lying, and that the Dark Jedi Master promised that this day would come, that the Jedi would attack Terrinak and try and kill their queen, after already poisoning her with their dark magics.

Reaching out with the Force, the Jedi learn that the queen is in a Force-induced coma. When Luke and Mara rouse her from the slumber, the Garsanekra realises the Dark Jedi Master has tricked it and the rest of its kind. The Dark Jedi had manipulated events, to force the Garsanekra into a position of power, as it is the only one of its kind who is Force-sensitive, and therefore able to communicate. Angry at this manipulation, the Garsanekra storms off to the hidden cavern where the Dark Jedi Master resides.

The two dark side users viciously attack each other with sabers and Force lightning. The Garsanekra is badly wounded but the Dark Jedi Master flees right into the path of Shanna and Rylo. The two young Jedi fight hard, but Rylo is knocked against the tunnel wall with a powerful Force push and slumps to the floor. As Shanna is about to be struck down, the Force ghost of Macan appears and distracts the Dark Jedi Master just long enough for Shanna and Rylo to reposition. They then fight in perfect unison to outclass their opponent, and Rylo strikes him down.

Rylo and Shanna thank Macan and embrace. Macan smiles, and gives them a little nod, before vanishing forever, just before Luke, Mara and the Garsanekra arrive.

Together, the Garsanekra and the Garron-Hinn queen regain control of their kind and the battle draws to a close. The Dark Jedi and the other mercenaries are rounded up. Shortly after, the Garsanekra dies of its wounds.

Meiden, who was defeated by Li New, but shown mercy, becomes the first Jedi student at Li New's new Jedi Academy, which is contained within the Star Destroyer that the Jedi took control of earlier.

After evaluating all of his actions since he joined the Jedi, Codan decides he is unworthy, and leaves the order. Instead, he goes back to his fighter pilot roots, and is given command of the squadrons that protect Li New's Star Destroyer, The Spirit Of Macan.