As the Jedi and the Republic focus on internal struggles, a new threat surfaces beyond the farthest reaches of the Outer Rim. An enemy appears from outside known space, bearing weapons and technology unlike anything New Republic scientists have ever seen. Suddenly, Luke, Mara, Leia, Han Solo, and Chewbacca, along with their children, are thrust again into battle. But this time, all their courage, sacrifice, and even the power of the Force itself, may not be enough.

No longer content with the destruction the Yuuzhan Vong have already sown, Warmaster Tsavong Lah has demanded the heads of all the Jedi. The Jedi Knights are in terrible danger, and none more so than the young students at the Jedi academy on Yavin 4. Impatient, and figuring that forgiveness is easier to come by than permission, Anakin Solo takes off for Yavin 4 in his X-wing.

Merciless attacks by an invincible alien force have left the New Republic reeling. Dozens of worlds have succumbed to occupation or annihilation, and even the Jedi Knights have tasted defeat. In these darkest of times, the noble Chewbacca is laid to rest, having died as heroically as he lived. A grief-stricken Han Solo is left to fit the pieces of his shattered soul back together before he loses everything: friends, family, and faith.

It is a perilous time for the New Republic. Just when unity is needed most, mistrust is on the rise. Even the Jedi feel the strain, as rogue elements rebel against Luke's leadership. When alien invaders known as the Yunnan Vong strike without warning, the New Republic is thrown on the defensive. Merciless warriors, the Yunnan Vong glory in torture. Their technology is as strange as it is deadly. Most ominous of all, they are impervious to the Force.

Luke Skywalker is worried: A handful of Jedi Knights, including his nephew and niece, Jaina and Jacen Solo, have disappeared into the Unknown Regions in response to a strange cry for help that only they could hear. Now the alien Chiss have angrily lodged a formal complaint, accusing the missing Jedi of meddling in a border dispute between the Chiss and an unidentified aggressor.