Summary by Steve Wilson
Admiral Thrawn takes over the Uxio planet system with the help of Jedi Master C'baoth.
Admiral Thrawn Jorus C'baoth
C'baoth orders Captain Pellaeon to have a clone made for him, but to not tell Thrawn. Pallaeon agrees to do as C'baoth says, but plans to report to Thrawn as soon as he can. Unfortunately for him, C'baoth makes him forget his plan.
Meanwhile, C'baoth senses Leia near the planet Filve. He sends an entire squadron of TIE fighters after the Millenium Falcon to try to capture her, but Han, Chewie, C-3PO, and Leia escape.
Leia Amidala Skywalker Han Solo
Luke Skywalker is on the planet of Berchest, in the city of Calius Saj Leeloo, looking for the clones the Empire is creating. He senses Talon Karrde is there and goes to talk to him. They are seen by Imperial officers, but allowed to leave per standing orders from Admiral Thrawn.
Luke Skywalker Talon Karrde
On Coruscant, Mara Jade wakes up from her month-long coma.She knows Luke saved her, but she's still hearing the Emperor's voice telling her to kill him.
Mara Jade Skywalker
Thrawn sets a course for Poderis, having learned from his spies that Luke is heading there. On planet, Luke spots Imperials following him and escapes off the planet.
On Coruscant, Leia gives birth to twins, Jaina and Jacen.
Jaina Solo Fel Jacen Solo (Darth Caedus)
In space, Karrde happens to meet a colleague friend of his named Tomas Gillespee who was on Ukio when the Empire took over. He's being chased by Imperials now, but they flee when they see both Karrde and Gillespee's back-up entourage of ships.
Samuel Tomas Gillespee
Luke travels to Honoghr, where Khabarakh and Ovkhevam help him replace his X-Wing's power cells.
The Empire attacks Nkllon, leaving Lando's Nomad City disabled. General Bel Iblis responds to his distress call and takes him to Coruscant.
Lando Calrissian Garm Bel Iblis
Imperials, led by Major Himron, infiltrate the palace on Coruscant attempting to kidnap Jaina and Jacen for C'baoth. Mara, Lando, Bel Iblis, Chewie, Leia, and Han kill them and capture Himron. Hirmon says Mara let them into the palace.
Meanwhile, Karrde, Gillespee, and Niles Ferrier meet with a group of other smugglers at the Whislter's Whirlpool Tapcafe on Trogan trying to convince them to help the New Republic. Some refuse until a squad of Stormtroopers attacks their meeting. After they dispatch the Imperials, the smugglers are all in.
Ferrier goes back and reports to Thrawn. The Admiral threatens to kill Thrawn for arranging the attack on the smugglers because now they are no longer neutral. He gives Ferrier one more chance, though, as he sends him to meet with the smugglers again to find out their plans. Thrawn sends Rukh with Ferrier to keep him in line.
On Coruscant, Colonel Bremen has Mara Jade under house arrest, despite Han and Leia's protests.
Colonel Jak Bremen
Mara tells Leia that the Imperial cloning facility is on Wayland.
Meanwhile, Karrde attacks and destroys a number of ships at the Empire's Bilbringi Shipyard.
Luke secretly brings a squad of Noghri, led by Cakhmaim, into the palace on Coruscant to protect Leia and the twins while Luke, Han, Chewie, Lando, and Threepio break Mara out of her cell and fly to Wayland.
C'baoth senses their move and travels to Wayland himself. Thrawn sends General Covell with him.
General Freja Covell
Despite C'baoth's "orders" (he wants to protect Leia and the twins), Thrawn attacks Coruscant. With Ackbar away, Mon Mothma asks Bel Iblis to command the Rebel forces. He accepts. Instead of attacking directly, though, Thrawn simply deploys a number of cloaked asteroids to orbit the planet, and then leaves. Coruscant can't lower its shield until it destroys the asteroids, effectively tying the Rebel's hands for a while.
Admiral Gial Ackbar Mon Mothma
During the battle, Ghent decrypts the transmission code of Delta Source.
Thrawn then has Captain Mazzic, one of Karrde's smuggler friends, captured and brought to him. Thrawn apologizes for the attack on Trogan, says he didn't authorize it, and then lets Mazzic go, implying that someone else paid the Imperial troops to attack the smugglers.
Once Mazzic leaves, Thrawn orders Ferrier to send his Defel to plant evidence on Karrde's ship showing that he hired the Imperials.
The group lands on Wayland and are attacked by garrals, animals that are attracted to engine noise, used by the Empire as watchdogs. Luke tells Mara how the Emperor died. She thought Luke killed him.
Leia finds Delta Source. It is a maintenance droid transmitting their conversations back to Thrawn.
Mazzic and Ferrier arrive separately to a meeting with the smugglers. Ferrier's Defel plants the data card on the Wild Karrde. Mazzic wants to inspect Karrde's data cards. Backing him up, Ferrier accidentally says too much, revealing that he knows details about the attack that he wouldn't otherwise know if he hadn't arranged it. When the others turn on him, he runs back to his ship, takes off, and launches a net on the Karrde to get it grounded while he escapes.
The group on Wayland meets another clan of Noghri led by Ekhrikhor. They have been guarding the group and have now stopped an attack on the group by the native Myneyrshi and Psadans. Settling for a peace negotiation, the two native groups agree to talk to the Rebels. They agree to let the Rebels pass to see if they can oust the Imperials from the planet.
C'baoth takes over Covell's mind on the way to Wayland, but when C'baoth comes into contact with the Ysalamiri, he loses contact with the Force and Covell dies, unable to think for himself any longer. Colonel Selid at Wayland reports this to Thrawn, who then orders Selid to put C'baoth under house arrest. Thrawn knows C'baoth is insane and no longer useful to him, but plans to clone him so that he can have his own Jedi.
Ysalamiri Kleyn Selid
Meanwhile, the Rebels on Coruscant need a Crystal Gravfield Trap to clear out the cloaked asteroids. They know that the Empire has two. Colonel Derlin plans to lead a diversionary attack against Tangrene while General Madine and Admiral Ackbar seize the one at the Bilbringi Shipyard.
Bren Derlin General Crix Madine
Admiral Thrawn guesses the plan, however, and is ready for their Bilbringi attack.
Karrde arrives at Coruscant to talk to Mara. Leia tells him she's on Wayland and asks him to take her there. Fey'lya pays him to do so.They arrive just as a group of Psadans storm the front entrance to Mount Tantiss demanding the release of C'baoth, and Luke's group breaks in a back entrance. Karrde has his two vornskrs, Drang and Sturm, with him to aid in the battle.
Borsk Fey'lya Drang
Luke and Mara find their way to the Emperor's throne room inside Mount Tantiss. C'baoth is waiting for them. Luke has discovered that the Jedi Master is actually a clone of the real C'baoth who is long dead. C'baoth presses a detonator, setting off a bomb that kills all the ysalamiri around the compound. He now has access to the Force again. C'baoth attacks and also orders a clone of Luke (made from Luke's severed hand and wielding the lightsaber he lost on Cloud City) to attack.
Leia, Han, and Karrde rush to the throne room. C'baoth knocks them out. Mara kills Luke's clone, thus fulfilling her mission to kill Luke Skywalker. She then kills C'baoth.
At Bilbringi, the Rebels attack, being led by Wedge Antilles. The smugglers (Gillespee, Mazzic, Karrde's crew), who planned to steal the crystral gravfield trap from the Empire and then sell it to the New Republic, are caught in the crossfire, not knowing that a battle was about to erupt when they arrived. The smugglers team up with the Rebels and steal the CGT while also defeating the Empire.
After the battle, Luke gives Mara his old lightsaber and she decides to join the Rebellion.