On the distant world Rhommamool, the invaders, through Nom Anor, disguised as the leader of the Red Knights of Life, stirred up rebellion between Rhommamool and its neighbor Osarian to distract the New Republic from its more important attacks. Around this time, a Praetorite Vong worldship commanded by Prefect Da'Gara touched down on the icy and unknown planet Helska 4, where they unloaded a massive, tentacled creature known as a yammosk, or "war coordinator".

It was by using this beast that the Yuuzhan Vong coordinated the attack on Sernpidal, using the ancient Yo'gand's Core tactic to crash the planet's moon Dobido into it, killing all Sernpidalians that had not managed to escape, as well as the famous Wookiee Chewbacca, who had been on a delivery run for Lando Calrissian. The Yuuzhan Vong eventually struck a deal with the Hutts that allowed them to pass through Hutt Space unharmed. But the Hutts were betrayed, and their worlds were attacked. The Peace Brigade, an organization of galactic beings that supported Yuuzhan Vong operations, was formed through Yuuzhan Vong agents. This organization also helped the Yuuzhan Vong capture Jedi. With Coruscant rapidly becoming surrounded, the Yuuzhan Vong created the fearsome voxyn beasts that hunted Force-sensitive individuals.

A Jedi strike team lead by Anakin Solo then destroyed the voxyn breeding facility, though most of the team was slain. Anakin himself died (or rather, disintegrated when his body overflowed with the Force) while he covered the retreat of the remaining Jedi. On Coruscant, the Yuuzhan Vong captured the planet after a long battle, which saw the suicide-sacrifice of Chief of State Borsk Fey'lya, and had it Vongformed, renaming it Yuuzhan'tar. The Yuuzhan Vong then began attacking worlds in their path with much ease. Bimmiel, Dantooine, and Obroa-Skai were among the many worlds captured while Ithor was turned into a fireball and rendered inhabitable. Soon arose the problem of refugees from shattered planets that the government could not ignore.

The government began to blame the Jedi for starting the conflict with the aliens. With the capture of Coruscant, the New Republic was thrown into disarray. Although localized victories were scored in the Hapes Cluster and other areas, the Vong fanned out throughout the galaxy, taking worlds almost at will. Planets that were not conquered outright often capitulated, or collapsed internally due to the efforts of collaborators. At this time, the Vong controlled most of the Core, the Inner Rim, and the galactic eastern area of the Mid and Outer Rims. The New Republic was reduced to a wedge of the southwest outer Rim, a small pocket connecting Kashyyyk and Mon Calamari, the Deep Core, and other minor areas. Following the conquest, Borleias became the capital world. The terraforming of Coruscant was sabotaged by the Jedi Knight Jacen Solo. The New Republic, having moved to Mon Calamari, where Cal Omas was elected Fey'lya's successor as President of the New Republic. The Defense Force then prepared to attack the weary Yuuzhan Vong. At the same time the Alpha Red Project, which would have destroyed the Yuuzhan Vong and their organic technology was destroyed by Vergere. Admiral Ackbar, though retired and advanced in age, began advising the reforming Defense Force and its commanders on the best ways to take the fight to the Yuuzhan Vong. Fleets were reorganized and new units were trained and equipped. The former Supreme Commander invigorated the beings in the New Republic military, giving them back their pride and confidence. After determining their weaknesses, Ackbar developed a trap for the Yuuzhan Vong. A large portion of their fleet was then lured into the Deep Core moon Ebaq 9, with a third of their force being decimated by several combined fleets of the New Republic.

On Ebaq 9 Tsavong Lah was slain by Jaina Solo and Vergere sacrificed herself to eliminate the rest of the invaders. At this point, the New Republic was reorganized as the Galactic Federation of Free Alliances, also called the Galactic Alliance. Incorporating a new federal system, the new Galactic Alliance focused itself to defeating the Vong threat and restoring peace to the galaxy. After the victory, Galactic Alliance heroes Han Solo, Leia Organa Solo and the Twin Suns Squadron headed out to find powerful allies while the Jedi Master Luke Skywalker began a mission to find the legendary living planet Zonama Sekot. The Jedi stumbled upon a Yuuzhan Vong attack against the Imperial Remnant and helped fight the invaders off, gaining a powerful ally.

Meanwhile, the Yuuzhan Vong Nom Anor disguised as the prophet Yu'Shaa began stirring up the heresy on Yuuzhan'tar (formerly Coruscant) posing as a Shamed One after fleeing the wrath of Supreme Overlord Shimrra for suggesting the disastrous Ebaq 9 mission. However, Yuuzhan Vong operatives stole one of Zonama Sekot's organic starships and the Shaper Nen Yim discovered that Sekotan technology was extremely similar to Yuuzhan Vong technology and that her people have gone terribly astray. Nom Anor disguised as Yu'Shaa along with Nen Yim and the priest Harrar arrived on Zonama Sekot where they discovered that many of the species from their galaxy could be found on the planet. A plot by Nom Anor to destroy the living world was luckily foiled. Han and Leia also managed to rescue hundreds of high-ranking Alliance prisoners facing sacrifice to the enemy's gods. The Galactic Alliance prepared a fleet to defend Mon Calamari from the invaders while another Alliance fleet engaged the Yuuzhan Vong at Coruscant. In the end, Supreme Overlord Shimrra was killed by Luke Skywalker and the Yuuzhan Vong were defeated. Warmaster Nas Choka ordered the Yuuzhan Vong to surrender, and they were placed under Zonama Sekot's jurisdiction.