Jacen Solo, son of Han Solo and Princess Leia, has escaped from the Yuuzhan Vong with the aid of prequel-generation Jedi Vergere. Besides making cryptic references to Jacen's destiny, Vergere also reveals that she's spent the last fifty years with the Vong in order to save the living world of Zonama Sekot as well as gather intelligence.
Luke Skywalker inducts nine Jedi Knights into the new Jedi order he is forming, among them Jacen, his sister Jaina Solo, and the Hapan queen Tenel Ka. The New Republic forces now assembled on the water world of Mon Calamari plan their next attack on the Yuuzhan Vong with the aid of the now-retired Admiral Ackbar.
However, some elements in the New Republic are desperate enough -- the Bothans especially -- to make the war against the Yuuzhan Vong one of extermination as well as victory. The success of the operation against Ebaq 9, a long-neglected world on a former Imperial trade route, leads the Vong into a trap that halts their advance. Vergere sacrifices herself to save Jacen by plowing a shuttle into Ebaq 9's surface.
The Yuuzhan Vong agent provacateur Nom Anor, who suggested the assault on Ebaq 9, is obliged to give his life for his plan's failure, but he disguises himself and hides beneath Yuuzhan'tar's (formerly Coruscant's) streets.