The Unifying Force

The novel begins on the Yuuzhan Vong prisoner-of-war camp planet of Selvaris. Four prisoners, a Jenet named Thorsh and three Bith, memorize a complex mathematical code smuggled in by a member of the Ryn Syndicate, and they make their escape. Two of the Bith are killed by the pursuing Yuuzhan Vong forces while one of them is captured, but Thorsh escapes Selvaris thanks to the Millennium Falcon. The surviving Bith is interrogated by the camp's head, Malik Carr, and the Bith reveals the mathematical code, unknowing of what it actually means. The Bith is killed as a result.

The Millennium Falcon brings Thorsh back to the Galactic Alliance where he is debriefed and recites the mathematical code to a Givin member of the Alliance. The code reveals that Selvaris will be the last pickup point for a Yuuzhan Vong-Peace Brigade convoy that will be taken to Yuuzhan'tar (Vongformed Coruscant) for a grand sacrifice. So an Alliance fleet ambushes Selvaris and rescues many prisoners, although some manage to get away. However, the Millennium Falcon, badly damaged from the battle, is forced to make an erratic jump into hyperspace that transports it to Caluula. As it turns out, the inhabitants of the Caluula system have been fending off the Vong for quite some time now, but they are able to repair the Falcon. Some of the prisoners leave the Falcon's company in order to help the residents of Caluula continue to fight the Yuuzhan Vong while the Falcon returns to the Alliance with what prisoners they have left.

As Zonama Sekot travels through hyperspace back to known space (it was previously in the Unknown Regions), it turns out that Harrar survived his confrontation with the treacherous Nom Anor in the previous novel. And through him, he and the residents of the living world discover that the Yuuzhan Vong exist outside the Force because they had been stripped of it, most likely by their homeworld of the original Yuuzhan'tar (which was destroyed in the Cremlevian War) back in the Vong's home galaxy.

On Yuuzhan'tar, things are not going well for Shimrra's order. Even with all of the advancements they made in the war against the Galactic Alliance, problems continue to plague the Yuuzhan Vong's capital planet thanks to the World Brain, and the heresy espoused by the Shamed Ones is still as strong as ever, even without Nom Anor's leadership. Nom Anor himself has been inducted back into the elite as Prefect of Yuuzhan'tar thanks to his actions on Zonama Sekot, but even he can't quell the fire that he sparked in the Shamed Ones as Yu'shaa, their Prophet. As for the sacrifice that had been partially foiled thanks to the Battle of Selvaris, the Yuuzhan Vong are able to compensate with captives from other contested worlds following Selvaris. But the sacrifice is spoiled thanks to a riot caused by the Shamed Ones, who save many of the Galactic Alliance captives much to their own detriment as Shimrra has many Shamed Ones and workers executed as capital punishment. Nevertheless, despite the thwarting of the sacrifice, Shimrra gives Warmaster Nas Choka the go-ahead to prepare his fleet to invade the Galactic Alliance's capital of Mon Calamari.

As the Yuuzhan Vong arrive at Mon Calamari and battle the opposing Galactic Alliance forces, Han and Leia Organa Solo, along with a few allies, infiltrate the Vong-captured Caluula in order to eliminate the resident yammosk there. Though they are captured with two of their allies killed, they find that the local Yuuzhan Vong and their biots are dying, along with many of Caluula's indigenous creatures. After many of the Yuuzhan Vong, their biots, and Caluula's own creatures die off, one craft made for Shimrra's new special Slayer warriors manages to make it off Caluula and it heads back to Yuuzhan'tar in order to inform the elite of this new affliction. As Kyp Durron, part of the infiltration team, is able to discern, the illness that the Yuuzhan Vong on Caluula are suffering is Alpha Red, a biological virus set to target and eliminate the Yuuzhan Vong and anything sharing their DNA with them. It had been deployed on Caluula in secret just before the planet surrendered to the invaders.

Just before it seems that Nas Choka's forces would win at the Battle of Mon Calamari, they suddenly make a hasty retreat back to Yuuzhan'tar, where Zonama Sekot has appeared in the capital planet's skies, causing various disasters and eliciting more opposition from the heretics. With the living world offering a distraction to the Yuuzhan Vong, the Jedi and the Galactic Alliance gather up all of their forces and resources for one last showdown against the Vong. After the Alliance successfully captures the Vong-occupied world of Corulag as their staging position, they travel to the captured Coruscant, and the Battle of Yuuzhan'tar, the final battle of the Yuuzhan Vong War, begins.

On the ground, Nom Anor decides to forsake Shimrra's order, seeing how deranged he has become as a result of Zonama Sekot's arrival, and realigns himself with the Shamed Ones against those who are still loyal to Shimrra. The heretics are soon reinforced by Galactic Alliance soldiers who managed to get past the Yuuzhan Vong's space defenses as the space fleets of both the Alliance and the Vong duel over the contested planetary capital of the galaxy and the world of Muscave. Meanwhile, Nas Choka takes a portion of his fleet to destroy Zonama Sekot using the Alpha Red-infected Slayer ship, as Shimrra revealed previously that there is indeed a biological connection between the Vong and Zonama. Defending the living world are the majority of the New Jedi Order, the Smugglers' Alliance, and the fleet of the Hapes Consortium. On Yuuzhan'tar, Luke Skywalker, his wife Mara, Jaina and Jacen Solo, Tahiri Veila, and Kenth Hamner all join up with Captain Judder Page's commandos in order to storm Shimrra's Citadel and kill the Supreme Overlord, ending the Yuuzhan Vong War once and for all. However, Mara, Tahiri, and Hamner all join a division of Page's commandos to help the heretics against Shimrra's loyal warriors, and it gives Mara an opportunity to confront Nom Anor, despite the fact that he is leading the heretics, for all he did to her, her family, and her friends and allies in the past. After Mara gives him a severe beating, Nom Anor pleads for his life, which Mara grudgingly spares so that he would be properly convicted for his crimes in the end.

Meanwhile, the Millennium Falcon goes on a mission with Harrar to convince the World Brain to cease its destruction of Yuuzhan'tar, which was intended by Shimrra to completely destroy the world so no one could have it, just to spite the Galactic Alliance. With the help of Nom Anor and his Shamed Ones and other allies, including turncoat Vong warriors, the crew of the Falcon, and Harrar, avert death from the Yuuzhan Vong sent to protect the World Brain. Then the Falcon's crew and Harrar make it to the dhuryam and they try to coerce Master Shaper Qelah Kwaad into convincing the brain to cease its destructive activities before they consider killing it. In the end, though, Jacen telepathically tells the World Brain to ignore Shimrra's commands, which stops Yuuzhan'tar's apocalypse.

As Page and his remaining commandos storm the lower levels of Shimrra's Citadel, Luke, Jaina, and Jacen, after killing and wounding every Yuuzhan Vong warrior in their path, eventually confront Shimrra and his fifteen special Slayer guards inside Shimrra's private coffer at the top of the Citadel. The three Jedi are able to kill all of the Slayers whilst Jaina follows Shimrra's Shamed companion, Onimi, to the control level of Shimrra's coffer. There, Onimi easily overpowers Jaina and renders her unconscious with a toxin from his fang. Jaina notes, as she falls unconscious, that she was able to sense Onimi through the Force. Meanwhile, with all of his Slayers dead, Shimrra fights Luke and traps him with his royal amphistaff, the Scepter of Power, before taking out the late Anakin Solo's lightsaber as a mind game to Luke; Shimrra wants Luke to know what it feels like to fight something that is part of his order, just as the Yuuzhan Vong have to fight Zonama Sekot, something that Shimrra believes should have been part of the Vong's order due to its living nature. Though Luke is poisoned by the Scepter of Power, he is able to take Anakin's lightsaber from Shimrra's grasp and he uses both his own and his late nephew's weapons to decapitate Shimrra. With Jacen's own lightsaber lost in the conflict, Luke throws him Anakin's lightsaber, which Jacen misses, and sees it fly away, echoing the vision he had on Duro three years earlier, and again on Zonama Sekot before the Battle of Yuuzhan'tar began. Regardless, Jacen goes up to the control level of Shimrra's coffer in order to collect Jaina.

As Onimi readies Shimrra's coffer to launch into space, an awakened but still weakened Jaina is told by the Shamed One, who believes that she is the human avatar of the Vong Trickster goddess Yun-Harla, that he had attained his Force powers by grafting yammosk DNA to his own neural tissue in order to emulate the gods' works in creating the universe. This was done after Onimi, being a Shaper at the time, discovered that there was no eighth cortex in the Shaper Qahsa. Although he was Shamed as a result, he was able to use his powers to not only concoct deadly toxins that he could control in his body, but he also manipulated Shimrra into convincing the rest of the Yuuzhan Vong into invading the galaxy; therefore, throughout Shimrra's reign, it was Onimi who had really been controlling the Yuuzhan Vong as its true Supreme Overlord. With Shimrra now dead, he plans to kill everyone and every living thing in the galaxy so that he could become a new god and fashion a new universe in his image.

As the Alliance and their Yuuzhan Vong allies take hold of Shimrra's Citadel, Luke is carried away, and Han and Leia follow Nom Anor's lead in order to find Jaina and Jacen at the control level of the Supreme Overlord's coffer. As they do that, the coffer launches for space, and the Millennium Falcon, piloted by Mara Jade Skywalker with an ailing Luke aboard, and Jagged Fel in his commandeered X-wing follow the coffer. Meanwhile, as word of Shimrra's death spreads, Nas Choka and his forces refuse to believe it, especially after his coffer appears rising up from Yuuzhan'tar. In the coffer, however, Jacen confronts Onimi and then hears the voice of his late grandfather, Anakin Skywalker, telling him to "stand firm," like he did on Duro. So as Jacen fights Onimi, he manages to achieve oneness with the Force, knowing that he'll never achieve this state again while simultaneously knowing that he'll spend the rest of his life trying to do so. As a result, Jacen defeats Supreme Overlord Onimi.

Han, Leia, and Nom Anor arrive just in time to watch Jacen's amazing victory as he appears to age five years. Onimi, meanwhile, is reverted of his Shamed deformities, but because his deformities were the result of his gaining the Force, he loses control of the toxins in his body and dies, melting into a puddle of foul hydrocarbons that is absorbed by the coffer's yorik coral floor like a stain.

The coffer begins to die off due its now-lost connection with Onimi, and Nom Anor tries to trick the Solos into going into a garbage chute while he escapes alive. With his Vongsense, Jacen thwarts his plan, and when Nom Anor tries one more time to evade the Solos, his hand is cut off by Leia via her lightsaber. Nevertheless, Nom Anor opens up the entry into the coffer's yorik-trema (landing craft) and simply allows the Solos to leave without him; due to his atheism, which makes him undesirable in the Yuuzhan Vong's society, and his contempt for the Force, which makes him undesirable in the Galactic Alliance's society, Nom Anor elects to die aboard the coffer, despite his earlier vows of surviving the war.

The coffer's explosion is viewed by Warmaster Nas Choka and his fleet. He announces to all of his forces that the war is over and that the Yuuzhan Vong's enemies have won. He offers them an ultimatum; those who wish to die may kill themselves or fight to the bitter end, while those like him will live to find out what the Galactic Alliance and their allies intend to do to them. Meanwhile, Zonama Sekot manages to repel the Alpha Red-infected Vong ship from its surface and brings down all ships, Yuuzhan Vong and non-Vong alike, to the ground. The Vong's weapons become docile and harmless as the invaders are welcomed home.

Aboard the Millennium Falcon, the Solos are saved from the dying yorik-trema, and Jacen is able to use Mara's tears and his own to concoct a chemical, as the late Vergere has done, to cure Luke of Shimrra's amphistaff poison. It works, and the Skywalkers and Solos collapse into one big embrace, glad that they survived and that the war is over. C-3PO and R2-D2 watch this scene and lament how at times like these, they envy how humans must feel.

Following the Yuuzhan Vong War's end, with most of the Peace Brigade dead and/or disbanded, Nas Choka meets with the Galactic Alliance's leaders to come to terms with how they should find a long-lasting solution to the war. Choka agrees to collect all remaining Vong throughout the galaxy so that they will be deposited on Zonama Sekot and be taken away into the Unknown Regions, where they will be safe and learn to acclimate their culture to peace and also reclaim their connection to the Force. To counter those who wish to see the Yuuzhan Vong totally exterminated, such as the Bothans among others, Galactic Alliance Chief of State Cal Omas saw to it that each and every remaining sample of Alpha Red has been destroyed. Meanwhile, Zonama Sekot discovers that it is the offspring of the original Yuuzhan'tar, thus explaining the biological connection that it has with the Yuuzhan Vong.

Amidst all of this, Luke declares that the Jedi shouldn't be the police force of the galaxy like it once was, and that the Order should allow individuals to find their own way in serving the galaxy, and, more importantly, themselves and the Force. Jacen, for one, plans to go on a galactic sojourn so that he could broaden his view of the Force following his battle with Onimi.

Several weeks later, after nearly every remaining Yuuzhan Vong is collected, Zonama Sekot travels back into the Unknown Regions. Later, the Skywalkers, the Solos, and their friends and allies revisit Kashyyyk, where Han pinions Anakin's lightsaber into Chewbacca's makeshift grave. Luke declares that should the need ever arise again, someone as virtuous as Chewbacca will pick up Anakin's lightsaber and conquer whatever threat that will endanger the galaxy in the future. Afterwards, they all have a feast where they discuss their vacation plans. Han convinces Lumpawaroo and Lowbacca not to carry on Chewbacca's life debt by saying that he and Leia already convinced their Noghri bodyguards, Cakhmaim and Meewalh, to take a vacation for themselves. The novel, and the series, ends with everybody laughing, not only at what Han said, but also in joy and relief that once again, the galaxy is at peace.

• Official CargoBay Listing
• The Unifying Force on Wookieepedia, a Star Wars wiki