Jacen Solo is hanging in the Embrace of Pain. Vergere is there playing with his mind. Jacen does not know how long he has been there... days, weeks, months, or years.
Vergere and Nom Anor want Jacen to become a true believer. Basically they want to convert him to the Vong way of thinking and everything they are doing is to meet that end.
Jacen is now let out of the Embrace of Pain. He learns that he is in the Vong Seed ship that is to populate the new Vong world based on the long lost Vong home world. There are 10 Dhuryoms(planet brains)on the ship practicing to run a planet. Vergere implants Jacen with a Slave Seed.
Jacen forms a partnership/relationship with the dhuryom that controls Jacen and his sector.
Jacen has gained the ability to control Vong creatures now. He has done this through the Slave Seed implanted in his chest. He is starting to "fight back."
Jacen uses his control over Vong creatures and his relationship with his Dhuryom to destroy the other 9 dhuryoms in the middle of the shapers trying to pick which of the 10 Dhuryoms will live and run the new Vong planet. Jacen is about to kill his dhuryom as well, but Vergere stops him with paralyzing tears. With Jacen out of action, the seed ship plants itself into Coruscant which is now called Yuuzhan'tar.
Jacen is now on Yuuzhan'tar. Vergere has removed the Slave Seed from his chest. Jacen is free... so to speak.
Jacen is on the move, with Vergere going along. The Shaper in charge of Yuuzhan'tar is after Jacen thanks to some prodding by Nom Anor.
Vergere sets up a confrontation between Jacen and the Vong. Jacen uses the force to hurt Vergere and kill most of the Vong. Jacen realizes the Dark Side is him... not that the Dark Side is some part of the force.
Jacen is now fighting demons in his head. He ends up being led into the stomach of some weird Vong beast.
Jacen finally makes it to his destination... the Solo apartment. He has a long talk with "Anakin." Vergere finds Jacen. Nom Anor and gang are with. Nom Anor gives Jacen Anakin's lightsaber. Offers Jacen the chance to fight or to go along with Vong. Jacen desides why not go along... he can always fight later.
Jedi Knight Ganner Rhysode has been tracking down rumors of Jacen Solo being on a huge refugee ship called a Camp Ship. Jacen is with Vong, it is a trap for Jaina. Jacen tries to get Ganner to leave before Ganner can find him. Once Ganner finds Jacen, Jacen is forced to take Ganner prisoner or the Vong would destroy the entire ship. Takes him back to Yuuzhan'tar.
Jacen is using Ganner to gain access to the world brain. The Vong and Jacen are ready to practice the ceremony that Jacen and Jaina are to go through when they perform for the gods. Jacen will use Ganner as Jaina's stand-in. Ganner goes along with it but is not sure he can trust Jacen.
Jacen and Ganner get inside the Well of the World Brain(old Senate chambers) and lock all of the Vong out. Jacen plans to teach the world brain which happens to the be Dhuryom he had the relationship with before. The Vong start to break in so Ganner goes to buy Jacen time with Anakin's lightsaber.
Ganner says "None Shall Pass" and challenges the Vong. The Vong start with one on one combat and then attack in larger groups as Ganner continues to kill every single Vong that comes against him. The force is flowing through Ganner... kills tons of Vong... but eventually is killed. Jacen is able to teach the world brain to love just before the world brain eats Jacen. Nom Anor goes for his escape vehicle, but Vergere turns on him. She has Jacen's lightsaber. Ties Nom up.
Jacen and Vergere escape from Yuuzhan'tar in Nom Anor's ship. They left him behind alive cause the warmaster will do more to Nom than they ever could. Jacen decides his path is as student and Vergere is his teacher. Jacen tells Vergere that the worldbrain will now do everything just a little bit different than the Vong want... this way they have to learn to comprimize. Jacen says Vong are fanactics that try to turn everything they touch into what they want instead of just leaving it as it is. Vergere thinks the student has surpassed the teacher. Jacen still does not reach out to others in with the Force yet.