Five years after the Battle of Endor, as the New Republic holds a fragile control of the galaxy, a new threat emerges. Having been posted so far away from action, Grand Admiral Thrawn, a cunning and intelligent Chiss commander, begins to gather his Imperial forces for a strategic attack on the New Republic. With the aid of Captain Gilad Pellaeon and Thrawn’s personal bodyguard Rukh, they begin to set in motion an almost unbeatable plan. They enlist the aid of a mad clone of Jorus C’baoth, a dead Jedi Master, and use the Emperor’s hidden weapons vault on the planet Wayland, which the clone guards. The chain of events caused major unrest in the New Republic.
Meanwhile, Luke Skywalker encounters Talon Karrde and his gang of smugglers. The smugglers capture him but do not turn him over to the Imperials. The smugglers take him in just as Han Solo and Lando Calrissian come to see Karrde on the New Republic’s interest to hire smugglers as traders. Then, as if things could not be worse, Grand Admiral Thrawn comes to visit Karrde just as Luke escapes. One of Karrde’s employees, Mara Jade, chases Luke deep into the forest, where both ships crashed. Mara attempts to kill Luke because she believes that he killed the Emperor five years earlier during the Battle of Endor, and Mara was the Emperor’s Hand at the time. However, she finds out that she needs Luke if she is to survive. Then Thrawn himself decides to interfere with Karrde’s rescue attempts and tries to catch Luke and Mara first. The result is a firefight between Imperial troops and Karrde’s men. In the end, Karrde wins, but has to evacuate his base. Han and Lando head to the shipyards at Sluis Van after they discover, thanks to Karrde, that Thrawn has plans there.
The insane Jedi clone from Wayland, Joruus C’baoth, comes out of isolation thanks to Thrawn and learns about Princess Leia’s unborn Jedi twin children. Thus, C’baoth decides he will train them in the ways of the Force, unintentionally the dark side due to his insanity. Basically, Leia’s unborn Jedi twins and Luke Skywalker will either join him or die. Luke and Leia are both pursued across the galaxy. Princess Leia is repeatedly hunted down by a species of aliens known as the Noghri. In order to keep her safe from more kidnap attempts and to give her a break from all the work in the New Republic, Han sends Leia and Chewbacca to the planet Kashyyyk, where the Wookiees can protect her. But Thrawn deduces the fact. Leia is again hunted down by the Noghri on Kashyyyk, but she has a plan. With Chewbacca’s help, she manages to escape, and one of the Noghri is captured. The Noghri, Khabarakh, recognizes her scent as that of a child of the Dark Lord Darth Vader, as the Noghri had apparently been secret bodyguards of the Sith Lord. Determined to discover more about the Noghri’s situation, Leia persuades him to bring her to his homeworld.
Meanwhile, the New Republic believes there is a spy among them that is leaking information on the New Republic’s actions and plans to the Imperials. It is only known as Delta Source.
Just as Han and Lando reach the shipyards of Sluis Van, Thrawn launches his planned assault on the location. With a cloaking device, Thrawn is able to give an element of surprise as his mole miners (stolen from Lando) attempt to bore into the hulls of ships at Sluis Van, and steal them. But it just so happens that Rogue Squadron is at the scene. They fight off the TIE fighters while Han and Lando hatch a brilliant plan to stop the theft of ships. Thrawn is defeated in his first major offensive.
The Imperials retreat and order is restored…for now.