As Han, Leia and Harrar are being prepped for sacrifice, a group of Shamed One’s enters the room lead by The Prophet, Nom Anor.  A group of Vong warriors enter the room, but instead of attacking the Shamed One’s they come to their aid and attack the others in the room!  Harrar says the tide has indeed turned.  They are able to escape and follow a Master Shaper towards the World Brain.

The beasts that are holding Jacen kick a hole in the building and allow the Jedi inside.  As they head inside the Citadel, the run up many flights of stairs fighting off Vong attacks along their way to Shimrra’s chamber.  Jacen can feel the World Brain is growing confused and reaching through the Force he realizes his parents are about to destroy it.

Han tells the shaper to control the World Brain or it will be destroyed.  The Brain stands down and Leia says that Jacen must have played a part in this.  The shaper mocks the idea and says Shimrra is responsible as he is also responsible for the impending destruction of Zonama Sekot (which Nom Anor confirms).

Over Zonama, the Vong are beginning to take control of the battle.  The Jedi’s new ships have stopped responding and they are concerned that perhaps the infected ship has already crashed on the planet.

Luke, Jaina, and Jacen reach Shimrra’s lair and are faced by fifteen slayers and Shimrra himself, the largest Vong Luke has ever seen.  Shimrra is also protected by a dovin basal that forces Luke to his knees, but Jacen overcomes them with his Vong sense. The Jedi and the Slayers begin a battle to the death.  The Jedi take the upper hand, but the room begins to shift violently back and forth as the World Brain has now sided with the Jedi.  Shimrra seems unfazed by the movement and heads off one direction and they notice Onimi heading further up the tower.  Jaina chases him into another chamber and she senses his coming attack, but she is unable to stop it.  He attacks and bites her and she begins to pass out, but not before realizing that she was able to sense him through the Force!

Jacen and Luke are both taking several hits during the battle, before Shimrra finally decides to enter the fray.  He knocks Jacen to the ground and grabs Luke with his amphistaff.  Luke fends off the head as Shimrra reveals Anakin’s lightsaber.  Using the Force, Luke pulls the blade from Shimrra’s hand and using both his own and Anakin’s he decapitates the Supreme Overlord, but not before being bitten himself!  As he lays dying, Luke tosses the blade to Jacen who misses the blade as he did during his vision on Duro and he runs after Jaina.

Nom Anor leads Han and the others towards the top of the Citadel to find Luke and the twins.  Nom Anor is overwhelmed at seeing Shimrra’s dead body.  They find Luke who has been poisoned by an amphistaff and is nearing death and tells them the twins went after Onimi.  The building begins shaking violently and Nom Anor tells them that the room is an escape pod that should only answer to Shimrra.  He begins to wonder if the Supreme Overlord is really dead.

Jaina has been captured by Onimi who is preparing to launch and angrily refers to her as Yun-Harla.  He questions why he has been punished for learning the truth of the eighth cortex and that the Yuuzhan Vong are doomed to extinction. He tells her that he was once a Master Shaper that experimented by placing yammosk cells into his own.  Like the yammosk, he was now able to control the minds of others on an even more effective level.  The cost was dire as he became a Shamed One.  Knowing that the New Republic galaxy was his chance, he has been using Shimrra as his puppet.  He sees Vong gods in several of the Jedi.  Jaina looks on helplessly as he proclaims that he will exterminate everything in the galaxy.

As Luke is carried out, Harrar announces to those gathered including many high Vong officials that Shimrra is dead.  They look to the sky as Shimrra’s escape vessel launches into the air.

Jacen arrives at the bridge of the ship and is greeted by Onimi who is directing the ship as a yammosk would.  Jacen realizes that it was Onimi that had made the building move, not the World Brain, and that he is the true Supreme Overlord.  The two are now open to each other as Onimi had regained the Force!  Jacen then realizes with astonishment that he can touch Zonama Sekot with his Vong sense!  Jacen hears a voice telling him to stand firm and understands that it is the voice of his grandfather, Anakin Skywalker! Onimi throws objects at Jacen but he easily blocks them.  He then attempts to use his tears as poisons as Vergere could, but Jacen has now truly released himself to the Force and his Vongsense and has become more powerful than he could ever imagine and more than he will ever be again.  He now understands that Yuuzhan Vong once lived in symbiosis with their homeworld, but their thirst for war had separated them from it and the Force. 

Han, Leia, and the others enter the room and see Jacen standing in a ball of blinding light as the Force and his Vongsense merge into one.  Onimi is pressed up against a wall.  Before their eyes, the power Jacen has ages him five years and his youth vanishes completely.  Onimi’s body begins to heal, but then his body dissolves away into liquid on the floor!  But because its owner is dead, the ship is dying.  Nom Anor leads them to an escape pod, but tries to poison them in the process.  Jacen blocks the poison and Leia cuts off Nom’s hand.  The Solos get on board the pod, but Nom Anor decides that he will stay behind.