The novel is set in 35 ABY, several years after the end of the Yuuzhan Vong War, and it introduces the titular Dark Nest Crisis.
After triumphing in Star Wars: The Unifying Force, the heroes of the New Jedi Order return in a dazzling new adventure!
Luke Skywalker is worried: A handful of Jedi Knights, including his nephew and niece, Jaina and Jacen Solo, have disappeared into the Unknown Regions in response to a strange cry for help that only they could hear. Now the alien Chiss have angrily lodged a formal complaint, accusing the missing Jedi of meddling in a border dispute between the Chiss and an unidentified aggressor.
Luke has no choice but to head to the Unknown Regions for serious damage control. Han and Leia follow, intent on protecting their children from what could be grave danger. But none of them are prepared for what they find when they reach their destination.
A colony of mysterious aliens is expanding toward the edge of Chiss space. The leader of the alien nest is resolute. Adept in the Force, he is drawing old friends to his side, compelling them to join the colony and meld their Force-abilities with his, even if it leads to all-out war....
Six years after the Yuuzhan Vong War ended, Jaina Solo, Lowbacca, Tesar Sebatyne, Tahiri Veila, Tekli, and Jacen Solo receive a call through the Force that lures them toward the Unknown Regions. They decide to heed this call.
On the (mostly) reformed Coruscant, the members of Luke Skywalker Masters' Council, which is the new Jedi Council of the New Jedi Order, are discussing the several problems in the galaxy created by the absences of the Jedi Knights, who have left their duties and are all survivors of the Mission to Myrkr during the Yuuzhan Vong War. An envoy from the Chiss Ascendancy, Mitt'swe'kleoni, appears before the Council to file a formal complaint of why the Myrkr survivors are involved in a border dispute with an unknown aggressor. When Luke tells the envoy that the Council has no knowledge of the Knights' involvement with this dispute, the envoy leaves. At the behest of Galactic Alliance Chief of State Cal Omas, Luke is prompted to take his wife, Mara, their son Ben, and Jedi Master Saba Sebatyne to head to the Unknown Regions in order to retrieve the Myrkr survivors. Meanwhile, the Jedi Council sends Kyp Durron to ask Han Solo and his wife, Leia, to fill in some of the role gaps created by the Jedi Knights' departures into the Unknown Regions. But instead of complying with this request, Han and Leia decide to head into the Unknown Regions, rendezvousing with Luke and Mara at a mysterious insect-like space station in order to look for the Knights as well. They receive the help of Captain Jae Juun and his copilot, Tarfang, to head to the planet Yoggoy to look for the Myrkr survivors. The Skywalker-Solo clan also learn of a species of humanoid bugs, later revealed to be the long-assumed-to-be-extinct Killik race, as well as groups of other beings called Joiners, humans and aliens from all over the galaxy who bonded with the Killiks to the point of sharing their telepathy with them. The members of the Skywalker-Solo clan are worried that this is what the Jedi Knights, especially Jaina and Jacen, may have become. Meanwhile, R2-D2 is having malfunctions that impede his abilities and activities.
On Yoggoy, the Skywalker-Solo clan learn that the Killiks are being led by Raynar Thul, another survivor of the Myrkr mission. He was thought to be dead when he was kidnapped by the Dark Jedi Lomi Plo and Welk aboard the Tachyon Flier from the Baanu Rass, which, piloted by Plo and Welk, abandoned the survivors to find another way off of the Baanu Rass before the latter party completed their mission of destroying the voxyn. Raynar reveals that he obviously survived the crash of the Tachyon Flier when it hit the planet, but he doesn't seem to remember Lomi Plo and Welk. He was saved from dying in the aftermath of the Crash by the Killiks when they turned him into a Joiner. However, his Force-sensitivity made him more than just a mere Joiner like all of the others; he became the UnuThul via integrating with the nest of Unu, leader of the entire Killik race, as he organized the once-disorderly species into a hive-mind known as the Colony. And during the war with the Yuuzhan Vong, UnuThul began a campaign to rest the nests of the Killiks in the Qoribu system, which is a light year away from Chiss space. Following the end of the Yuuzhan Vong War, UnuThul used his Force call to gather up the survivors of Myrkr in order to help him in the Killiks' border dispute against the Chiss. After UnuThul's exposition, the Skywalker-Solo clan visits the Flier Crash site, where Leia sees a vision of Jacen revealing the location of the Killik nests (UnuThul didn't specify where the nests were located in his exposition). This vision stems from Jacen's earlier visit to Yoggoy to investigate the Crash, where he flow-walked back in time when the Crash occurred in order to find a horribly burned Raynar saving a similarly burned Lomi Plo and Welk from the flames of the wrecked freighter. After that, the Skywalkers, Solos, and Saba are attacked by blue Killiks. Though they survive the attack, they question UnuThul of what happened, to which he denies any knowledge of. The clan, now suspicious of the Killiks' motives, decide to leave Yoggoy for Qoribu.
At Qoribu, the Myrkr survivors, teamed up with the Killiks, battle Chiss forces around the nests. The Skywalker-Solo clan arrive in-system and are again attacked by Killik forces. This makes Luke nearly drain himself of his energy through the Force in order to defend the Jade Shadow, giving him an almost sickly appearance of the late Palpatine. The Skywalker-Solo clan make it through the attack and join down on Jwlio, one of Qoribu's moons made for the nest of the Taat, a Killik division, after the battle ends. They meet up with the Myrkr survivors, who reveal what the Killiks do in order to survive. The survivors justify their actions in risking negative relations between the Galactic Alliance and the Chiss by defending the Killiks, who are nothing more than a displaced species trying to find a permanent home in the galaxy. The Skywalker-Solo clan try to convince the survivors to come with them, leave the Killiks behind, and let the Masters' Council find another way to resolve the Killik-Chiss dispute before it escalates to total war. Jacen, Tahiri, Tekli, and Tesar decide to go with Luke, Mara, Ben, and Saba back to the New Jedi Temple on Ossus to see how the Killiks gather up Joiners. Alema Rar decides to go with Han and Leia. Jaina and Zekk decide to stay behind, if only to save Lowbacca, who was lost in space during the recent battle against the Chiss. But before the parties leave for Ossus, Saba is attacked in a cave by Welk and a few of the blue Killiks, which UnuThul still denies any knowledge of, and Saba is severely wounded, with Welk escaping her grasp. The parties are all aware that at least Welk, if not Lomi Plo, also survived the Yoggoy Crash, and UnuThul refuses to believe this. Regardless, the parties leave with the Jedi Knights they have. But Saba, in her wounded state, who is being taken by Han and Leia, fails to divulge the hypothesized information she thought of after her fight with Welk; that one of the blue Killiks has sneaked aboard the Jade Shadow with Luke, Mara, and Ben aboard. And on the Shadow, Ben gets into trouble for eating too much gelmeat by Mara, who thinks that Ben is lying when he says that he is feeding the gelmeat to his new Killik pet/friend. Meanwhile, Luke decides to fix R2-D2 in order to find out what's wrong with his functions, and finds a recording of his late father, Anakin Skywalker, and a woman who Luke suspects of being his mother. Artoo ends the recording, saying that it's a malfunction to his programming, but Luke doesn't believe in the astromech droid, wondering why he'd keep the information of his parents so secret.
Meanwhile, aboard the Millennium Falcon, Leia subtly tries to coerce information from Alema as to why she decided to go aboard, especially since Alema decided this just after Saba was wounded, and to the surprise of Jaina and Zekk—something that shouldn't happen within a hive mind. When Leia presses too hard, Alema demands that "you follow our demands," giving Leia the information she needed to know that Alema has been completely taken over by the Killiks. Later, the Falcon is sabotaged, secretly by Alema, and they land on a planet that is amidst a group of other planets in a nebula. Leia and Alema decide to investigate the "malfunction" of the Falcon when Alema turns against Leia and tries to escape. She fights Leia and her Noghri bodyguards, Cakhmaim and Meewalh. But though the bodyguards are defeated, Han manages to activate an escape pod, which knocks Alema unconscious. After repairing the Falcon, they bring Alema back to Ossus with the other Jedi Knights in Luke's company in order to see what's wrong with her.
On Ossus, medical healer and Jedi Master Cilghal examines the Jedi taken by Luke and Mara, and finds that the Killiks and the Joiners are all interconnected through a limited kind of telepathy that only works when the members of the nests are in close proximity to each other. And before the Jedi are tested for this, Saba awakens and warns Luke and Mara about the supposed blue Killik aboard the Jade Shadow. Realizing that Ben wasn't lying about the gelmeat, Mara confronts Ben and the blue Killik, whose nest is that of the Gorog. Mara and the Gorog fight, and she defeats it. The Jedi taken by Luke and Mara are further tested for their connection, and Alema and the Gorog are also tested. They find that Alema and the Gorog are more closely linked than the other Jedi are to the Gorog. Cilghal postulates that UnuThul denies all knowledge of the Gorog not because he's lying about their existence, but because he doesn't know. Cilghal states that the Gorog are most likely the unconscious part of the Killik nest, who operate without the knowledge of UnuThul, thus the attacks upon the Skywalker-Solo clan denied by the former Raynar. So the Gorog must be controlled by an outside party, most likely by Lomi Plo, and definitely by Welk. And Alema is among them because the Gorog had taken advantage of her grief over her late sister, Numa, and manipulated that grief to join the nest via the dark side anger that Alema pented up over the years. Knowing that the Gorog, or the Dark Nest (nickname for them by the Jedi), are controlling UnuThul to lead the Killiks into war against the Chiss, the Jedi figure that the Dark Nest must be stopped before terrible bloodshed occurs. In order to do this, they allow Alema and the Gorog who Mara defeated to steal a ship so that they could follow it via tracking beacon to where the Gorog nest is located. But before they do follow her, the hacker known as Zakarisz Ghent manages another recording from R2-D2 that depicts a conversation between Luke and Leia's supposed mother, whose name is revealed to be Padmé, and a younger Obi-Wan Kenobi, who tells Padmé that he is aware of the love between her and Anakin.
Meanwhile, the Killiks receive the help of the Hapes Consortium thanks to a visit to Hapes by Jacen, who persuaded Queen Mother Tenel Ka Djo, the only Myrkr survivor to refuse the call of UnuThul through the Force by locking herself in her own home, to give the Killiks the backup forces that they need to counter the Chiss offensive. Jacen convinces Tenel Ka to do this by spending the night with her. And Tesar receives the help of Raynar's mother, Aryn, to help the Killiks, especially since her son is leading the prime forces against the Chiss. Lowbacca, in the meantime, is captured by Chiss forces, led by Jagged Fel.
At Qoribu, when the Killik-Chiss conflict is at its height thanks to Raynar's mother's forces and the forces of the Hapes Consortium, the Skywalker-Solo clan track Alema and her Gorog companion to the Qoribu moon of Kr. There, while Han and Leia busy themselves between Hapan and Chiss forces as the Battle of Qoribu and the Battle of Kr commence, Luke and Mara follow Alema and the Gorog into an underground cavern inside Kr. They then fight off many Gorog insects just to get to the prime nest, and when they do, they battle several more Gorog, Alema, and Welk. The Millennium Falcon manages to get to the Kr underground lair with a few YVH droids and Jedi Masters. Many Gorog are killed by the invading forces of the Skywalker-Solo clan, Alema escapes after Luke cuts her arm off with his lightsaber, and Welk is killed in single combat via lightsaber duel by the Jedi Master. After the Chiss are told about the nature of the conflict, they stand down and UnuThul investigates the incident at Kr. He is shocked to find that the Gorog nest does exist, producing their larvae through Chiss captives, as well as eating those captives, which explains the Dark Nest's motivation for going to war with the Chiss. UnuThul finds that he is indirectly responsible for its existence by saving Lomi Plo and Welk from the Crash, though the others try to tell him otherwise. The next step from here, UnuThul agrees, is for the Killiks who are not Gorog to build temporary nests aboard Hapan fighters until they are relocated to their new home at the set of planets Han and Leia visited before Leia had to fight Alema. Afterward, the Chiss return Lowbacca, and UnuThul severs the Joiner connection between the Jedi Knights and the Killiks, since they served their purpose of helping the race against the Chiss. However, Jaina and Zekk still have a powerful Force connection between each other from the Killik-Chiss conflict that disallows them to separate, and they can even read each other's minds. This serves as an awkward stance in Jaina's relationship with Jag Fel.
Han and Leia both agree that Leia's place is not as the copilot of the Millennium Falcon, and that Jae Juun, who has been with them since before Yoggoy, can easily replace Leia as the copilot. However, despite her professionalism as a politician, she doesn't want to return to government, having sworn politics out of her life before the Yuuzhan Vong captured Coruscant during the war against them. So she chooses the one remaining alternative left to her—she decides to be taught as a Jedi under the teachings of Saba Sebatyne, something she promised Luke she'd do years earlier, since before the Thrawn campaign.
- ISBN 9780345463043; July 26, 2005; Del Rey; US paperback
- ISBN 9780345463142; December 6, 2005; Del Rey; US eBook
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