Battle of Yuuzhan'tar

The Yuuzhan Vong experienced widespread panic and awe upon the arrival of Zonama Sekot. Yu'shaa, the prophet who was secretly Nom Anor, had been telling the Shamed Ones that Sekot's arrival would mean the end of the Elite's oppression. Believing their time had come, the Shamed Ones openly rebelled, which split the forces of the Warrior caste. The dispersion of the Rainbow Bridge of asteroids by Zonama Sekot also forced the planet's Dovin basals to focus on preventing asteroids from hitting the planet. Warmaster Nas Choka, already engaged at Mon Calamari, commanded the Yuuzhan Vong fleet to return to Yuuzhan'tar and recalled troops from many other planets within the Yuuzhan Vong empire. However, some Domains defied the order, fearing an attack on Zonama Sekot. Despite this, Choka managed to gather a large force, ready to confront the planetary intruder. Once assembled, Shimrra Jamaane, the Supreme Overlord of the Yuuzhan Vong, instructed them to maintain their position.

Shimrra was deeply afraid of Zonama Sekot. His ascension to the throne was the result of overthrowing Supreme Overlord Quoreal, who had hesitated to invade because of Zonama Sekot's presence. However, Shimrra reasoned that since its technology was like Yuuzhan Vong Shaping protocols, it could be vulnerable to things designed to attack the Yuuzhan Vong. Therefore, Shimrra ordered a Slayer ship infected with the Alpha Red virus to crash into Zonama Sekot.

But matters worsened for Shimrra. Sekot had provided the Jedi Knights with Zonama Sekotan fighters, living vessels similar to the Yuuzhan Vong's ships. Claiming that the Gods had given Sekot the Vessels as punishment for allowing the Jeedai heresy to continue, Shimrra ordered the immediate execution of all Shamed Ones, placing Nom Anor in charge of the execution squads. However, seemingly expecting defeat, Shimrra commanded the World Brain to start a series of fires and earthquakes that would eventually make the planet uninhabitable. Anor, believing Shimrra was insane, defected to the Shamed Ones.

In the meantime, the Galactic Alliance Defense Fleet rushed to Yuuzhan'tar and opened fire on the dovin basal screen protecting the planet. Many battle groups jumped to hyperspace from Mon Calamari, Eriadu, Hapes, and other planets, focusing their ships on planets near Yuuzhan'tar, like Muscave and Stentat. The Jedi arrived at Zonama Sekot and met with Master Luke Skywalker, who informed them of the events since his team began their search for the legendary world. Some Jedi, including Kyp Durron, Corran Horn, and Alema Rar, were chosen by Sekot to pilot Zonama Sekotan Fighters; however, Jaina Solo was not. She was to be part of a Jedi team that would enter the planet's surface, along with Luke, Mara Jade, Kenth Hamner, Jacen Solo, and Tahiri Veila. The reasoning was that the psychological impact of seeing the Solo twins together on Yuuzhan'tar would affect the superstitious Yuuzhan Vong. Simultaneously, Han and Leia Solo and the Yuuzhan Vong priest Harrar would go to the Well of the World Brain to neutralize the dhuryam, as Shimrra could use him to destroy Yuuzhan'tar.

The Supreme Overlord was doing just that. He convinced the World Brain to cause great fires to cleanse the areas damaged by groundquakes and magma streams to remove the fallen buildings. The World Brain had to follow Shimrra's orders but was aware that he was causing significant damage to the planet he was created to protect. From space, Warmaster Nas Choka could see the damage to Yuuzhan'tar, but he trusted that Shimrra would handle it, and his only concern was stopping the Alliance assault. Choka ordered the Alpha Red-infected Slayer ship to be ingested by a larger warship, ensuring its safe arrival at Zonama Sekot to poison the planet.

With large portions of the Yuuzhan Vong fleet fighting Alliance forces on other planets in the system, Yuuzhan'tar was relatively unprotected, and its defensive screen of dovin basals was fully occupied stopping asteroids from falling. Even so, the fighting was intense, and many ships were destroyed. Three transports carried Page's Commandos and other ground forces, but one was destroyed in space, and another crashed on the surface. Nevertheless, the Alliance successfully deployed soldiers on Yuuzhan'tar, and several starfighters broke through the dovin basal screen to attack planetary objectives.

On the streets and squares of Yuuzhan'tar, the heretics and Shamed Ones rebelled against the Elite. Though poorly armed, their numbers were so great that the warriors sent to kill them struggled. The Millennium Falcon arrived on the surface, and its crew reunited with the ground force commanders, with several commandos helping the heretics and Shamed Ones. Luke asked Mara to join them, and she reluctantly agreed, taking Tahiri and Kenth with her. The Yuuzhan Vong rebels were being overwhelmed, but the Alliance reinforcements arrived to support them. Seeing the Jedi boosted the heretics' morale, and they fiercely attacked the warriors, who were now trapped between two forces. Tahiri spotted Nom Anor, and Mara pursued him, eventually defeating and capturing him.

Han, Leia, their Noghri bodyguards, Harrar, and the droids R2-D2 and C-3PO boarded the Millennium Falcon to reach the Well of the World Brain. The only entrance was a maze of thorns as hard as durasteel with a potent neurotoxin, but Han Solo's piloting skills allowed the Falcon to reach the atrium. There, High Priest Jakan, High Prefect Drathul, and Master Shaper Qelah Kwaad were about to sacrifice several captives, and their warriors captured the Solos and Harrar to sacrifice them as well. A small group of heretics arrived, but they were only two dozen poorly armed rebels against fifty capable warriors. Among the heretics were Mara, Tahiri, and Kenth, guided by Nom Anor. Before the groups could engage, fifty more warriors arrived, and the heretics and Solos lost all hope. Fortunately, the new arrivals joined the heretics, and together they defeated the Elite's forces. Nom Anor killed Drathul, and Harrar overpowered Jakan and captured Kwaad.

On Zonama Sekot, the Jedi flew their fighters to protect the planet, but the living ships took time for the pilots to get used to, and vice versa. Sekot's defenses effectively repelled the enemy yorik-ets, but the number of adversaries continued to grow. In space, the fighting remained intense, with thousands of Yuuzhan Vong warriors and Galactic Alliance soldiers dying each minute. Nas Choka was satisfied, believing it was only a matter of time before the Alpha Red-infected ship reached the planet, ending the war.

Meanwhile, Luke, Jacen, Jaina, and Page's Commandos were approaching Shimrra's Citadel. The Jedi used the Force for assistance in their jumps, and the commandos followed as best they could with their jetpacks. However, at one point, the road was blocked by Tu-Scart and Sgauru, the massive battle beasts that had destroyed refugee settlements on Duro three years prior. The attacks by Chazrach slave troops and rakamats were constant. Jacen communicated with the World Brain to convince the war beasts to stop their attacks. Jacen and the World Brain had a special connection, as Jacen had chosen the dhuryam that would shape Yuuzhan'tar, making him the only one who could persuade the World Brain to disobey Shimrra. The World Brain was angered by the heretics' arrival at the Well, fearing they would kill him. Nevertheless, Jacen convinced him to side with the Galactic Alliance to end the war, and his destructive actions ceased. The World Brain ordered Tu-Scart and Sgauru to help Jacen, allowing the Jedi to enter the Citadel. The Chazrach, angered by the war beasts' apparent betrayal, attacked them. The rakamats, feeling betrayed because the Chazrach were attacking Tu-Scart and Sgauru, attacked them in turn, and soon the area around the Citadel was under Alliance control.

On Zonama Sekot, the Jedi fighters abruptly descended to the surface, perplexing the Jedi. No one could explain what had happened, but the Smugglers' Alliance had told them about the Alpha Red-infected ship, and everyone feared the worst: that the ship had reached the planet. Corran Horn believed Sekot was trying to contain the Alpha Red to prevent its spread, but the Jedi on Zonama Sekot were temporarily out of the battle.

Shimrra was informed that the Jedi had arrived at the Citadel and ordered his Slayers to let them enter, wanting to witness their deaths. The three Jedi went through seldom-used paths and encountered few warriors, but when they reached Shimrra, the Supreme Overlord was protected by fifteen Slayers. These modified warriors were so powerful that even Kyp Durron couldn't defeat one on Caluula, but the three Jedi proved the Force was with them and defeated several. They were aided by the Citadel's spontaneous tremors, which caused the Slayers to lose balance, giving the Jedi an advantage. During the fighting, Jaina noticed Onimi behind Shimrra and, following her instincts, went after him. Luke and Jacen didn't understand Jaina's departure, and the Slayers still outnumbered them. Wounded, the Jedi continued fighting, and Luke became a maelstrom of the Force, keeping their enemies at bay. Jaina was ambushed by Onimi, who poisoned her with his enormous fang. Jaina was shocked, but before Onimi knocked her down, she sensed him through the Force.

Meanwhile, Galactic Alliance reinforcements arrived in the Coruscant system, including Admiral Traest Kre'fey's forces. The space battle was going poorly for the Galactic Alliance, though the Yuuzhan Vong also suffered heavy losses. Since the battle's start, the fleets of Generals Wedge Antilles and Keyan Farlander had been under constant attack, but Alliance reinforcements kept arriving to even the field. However, Warmaster Choka remained confident that the Gods would not abandon the Yuuzhan Vong with victory so close.

Inside the Citadel, Shimrra moved to attack Luke Skywalker. The Supreme Overlord was immense and powerful, the greatest warrior of the Yuuzhan Vong. He wielded a special amphistaff, the Scepter of Power, larger and more powerful than common ones, which he used to poison Luke. With the Scepter asphyxiating the Jedi Master, Shimrra, to Luke and Jacen's amazement, produced Anakin Solo's lightsaber, intending to kill his hated foe with his kinsman's weapon. Nevertheless, Luke cut the Scepter of Power with his own lightsaber and, using the Force to pull Anakin's, used both sabers to behead the astonished Shimrra. Jacen wanted to help his uncle, visibly affected by the powerful poison, but was instead instructed to go after Jaina.

Han, Leia, Mara, Tahiri, and Kenth were guided by Nom Anor to Shimrra's throne, where they found the wounded Jedi Master and the dead Supreme Overlord. This sight shocked the executor, as the Yuuzhan Vong had never been without a Supreme Overlord. While Mara and Tahiri took Luke, Han, Leia, and Anor went after the Solo twins and Onimi, but at that moment, the Citadel rose into space at Onimi's command. Not knowing about Shimrra's death, Nas Choka thought the Citadel's arrival was his Supreme Overlord's personal support, renewing his warrior's spirit. Meanwhile, Sekot told Danni Quee that its only interest was to welcome home the Yuuzhan Vong, stunning everyone present, Jedi and Ferroan alike.

Onimi had tied Jaina's hands and, calling her "Yun-Harla," told her his story: when he implanted yammosk neural tissue in his brain, he gained the power to control others, even Shimrra, making him the true power behind the throne. Nevertheless, his experiments made him a Shamed One, which he blamed on Jaina-Yun-Harla and the other Gods, whom he hated. As the true Supreme Overlord, Onimi intended to kill Zonama Sekot, believing it would grant him the powers of a god, and kill every living being in the galaxy as well. Jacen arrived to confront Onimi, who could create toxins and poisons by manipulating his body's chemicals, but Jacen entered a state of oneness with the Force and, shining with its full power, neutralized all the venoms Onimi threw at him. Jacen's power was so great that he reverted Onimi's deformities, reversing the latter's use of the Force, and his foe died victim of his own unchecked poisons, dissolving him completely. Han, Leia, and Anor arrived just in time to see Jacen's victory.

With the death of the true Supreme Overlord, the ship they were in began to die, and Nom Anor guided the Solo family to a waste disposal system, making them believe they were going to an escape pod. However, Jacen discovered his deceit and stood in front of Anor's plaeryin bol poison, directed at his father and sister. Leia cut the treacherous executor's hand with her lightsaber, stopping him from releasing a gas that would render them unconscious to die with the Citadel. Jacen and Han offered Nom Anor another chance to go with them, but he refused, saying he wanted no part in what was going to happen next, and he chose to die with Onimi. The Solos used the escape pod, which was picked up by Mara Jade, piloting the Falcon. Inside the ship, Jacen, at Vergere's suggestion, used Mara's tears and his own to make an antidote to Shimrra's Scepter poison, saving Luke. Meanwhile, Zonama Sekot released small insectile craft that took the Slayer ship to deep space, saving the planet from destruction.

Witnessing the destruction of Shimrra's Citadel, Nas Choka knew that the Supreme Overlord of the Yuuzhan Vong was dead, and therefore the gods had abandoned them. Horrified, the Warmaster communicated with his Supreme Commanders and told them that, as the gods had abandoned the Yuuzhan Vong, anyone who wished to fight to the death or commit suicide was allowed to do so, and he himself would surrender to the Galactic Alliance. Most of his command staff chose death, and shortly after Nas Choka's transmission ended, many opened themselves with coufees, and hundreds (or thousands) of coralskippers and pickets became living missiles, hurling themselves towards Alliance vessels.

The Liberation of Coruscant was a success, and the planet was renamed Coruscant once more. Many Yuuzhan Vong survivors surrendered, shocked by what had happened, while others vowed to fight to the death. Warmaster Choka formally surrendered to the Alliance and reluctantly accepted the Yuuzhan Vong's exile to Zonama Sekot, revealed as the heir of their long-lost home, Yuuzhan'tar. The Sekot Accords were the peace treaty that finally ended the war. However, Coruscant had been heavily Vongformed, and while there was still a substantial amount of working technology beneath the foliage, it would take many years to become habitable again. Many Yuuzhan Vong refused Nas Choka's call to surrender and continued fighting for several more months.

While the war had been won, the casualties on the Galactic Alliance's side were incalculable. In the final battle alone, five million were killed, and ten million were wounded; the death toll of four years of war was said to be 365 trillion. Dozens of planets were devastated – Vongformed like Tynna, ravaged like Ithor, or completely destroyed like Sernpidal. Many species went extinct, and millions remained homeless refugees. Additionally, remnants of Yuuzhan Vong activity, such as dovin basal mines, were scattered throughout the galaxy. Nevertheless, the galaxy had united as never before, and the main factions and governments worked together toward a common goal. The Alliance had much work ahead, but the will to do it was present.

The planning team for the Star Wars: The New Jedi Order book series, including James Luceno, discussed whether to eliminate the Yuuzhan Vong species at the series' conclusion. They ultimately chose to exile the Vong, believing that a merciful option would be more interesting, less stereotypical, and more in line with the saga and series' spirit.