It's been a year since Chewbacca's death and our heroes' first encounter with the Yuuzhan Vong. Jaina Solo has joined Rogue Squadron. Mara Jade Skywalker's disease has been eliminated, and she is on Yavin 4, recuperating and continuing with Anakin's training. Han Solo, having returned from a journey into the Outer Rim to exact vengeance on the Vong for the death of his Wookiee comrade, requests reinstatement into the New Republic armed forces. He is eager to take the fight back to the Vong, but Chief of State Fey'lya still refuses to accept the aliens as a real threat.
Many small events of this nature finally add up, and Leia Organa Solo, Han, and Luke Skywalker (a large faction of the Jedi Knights along with him) renounce their affiliation with the New Republic. They start gathering forces and allies (among them Admiral Traest Kre'fey and Rogue Squadron), and prepare their own offense for the sake of the galaxy.
Jacen Solo, while being for the most part on his family's side, disagrees vehemently with their decision to separate themselves from the Galactic Government. He is forced to side with Kyp Durron, and stays behind on Coruscant. When he learns that Danni Quee (who is off with Organa Solo and the rest) has been killed by the Vong, it drives him over the edge, and he turns to the Dark Side. In Jacen's eyes, his newfound evil power is the only way to stop this tragedy from happening to others...
UPDATE: 8/28/000 - I've gotten many e-mails regarding what I said here. If you're reading this, please understand that it was all speculation; stuff I thought up months ago. It's now known that the whole scenario is almost definitely wrong. So please don't e-mail me asking if it's real.