The book continues a short time after the events of Heir to the Empire .
Prior to the Clone Wars, the Old Republic had constructed a fleet of 200 Dreadnaughts (huge forerunners to Imperial Star Destroyers) that were highly automated. This reduced their crew complement from 16,000 to 2,000 without diminishing their firepower. The flagship of this fleet was the Katana and hence became known as the Katana fleet. Unfortunately, a virus infected the crews of the entire fleet and drove them insane. The madness caused the crews to "slave" the controls of all ships in the fleet to the Katana and send them all into hyperspace. The fleet was never seen again until veteran smuggler Talon Karrde discovers it through a lucky accident several years before the events of the first book.
Now having full access to Emperor Palpatine's private storehouse on the planet Wayland, Imperial Navy Grand Admiral Thrawn presses his advantage to marshal more forces for the battle against the New Republic. When his forces capture one of Karrde's colleagues who also knew where the fleet was, he assembles a clone army from the storehouse to take over the fleet.
Han Solo and Lando Calrissian try to recruit former Republic Senator Garm Bel Iblis to join the fight against the Empire. However, the two face stern opposition from him because he fell out with Mon Mothma in the early stages of the Rebellion and waged his own private war against the Empire. They also discover that Bel Iblis' fleet also has Katana warships.
Elsewhere, Jedi Master Joruus C’baoth uses the Force to summon Luke Skywalker. Luke responds to the summons and begins instruction with C’baoth on the planet Jomark. However, the presence of Mara Jade complicates things further, especially when it is revealed that she was a former agent of the Emperor.
With Noghri captive Khabarakh in tow, Leia, C-3PO and Chewbacca travel to Khabarakh's home planet of Honoghr. She learns of the Empire's deception of the Noghri and convinces them to support the New Republic.
After escaping C'baoth, Luke rejoins Lando and Han in securing the Katana fleet against Thrawn's troops. However, over the course of the battle, they find out that Thrawn has captured all but 15 of the Dreadnaughts. Mara is also knocked out during the fight when her fighter is shot down.