While the events of the comic coincide with the events of the novel, the comic does not follow much the exploits of Leia, Lando and the mysterious villainess Guri, who here plays only a minor supportive role; on the other hand it includes a generous amount of what Boba Fett was up to during that time, the rivalry with his fellow bounty hunters, and Jix's mission on Tatooine.
Aboard the Redemption, Leia is informed that Imperials have spotted the Rebels, and Rogue Squadron led by Wedge Antilles begins defending the Rebel side in a space battle so that their point remains secret. Leia meanwhile understands that Luke is different after his encounter with Vader and wonders what happened between them.
On the Executor, Sidious contacts Darth Vader and chastises him for his failure on Bespin. He then orders Vader to conclude shipping arrangements of the Death Star II plans with the Black Sun crimelord Prince Xizor. On his way out, Xizor explains to Guri, that he intends to kill Luke and improve his prestige to the Emperor, while also discrediting Vader. Guri has made her arrangements with bounty hunters and Xizor is ready to meet Jabba.
Above Tatooine, Boba Fett who carries Han Solo in carbonite, exits hyperspace but discovers that a signal beacon -installed when he was on Cloud City- was activated; he has a dangerous encounter with IG-88D who intended to claim the bounty of Solo. Fett energizes the inertial dampers and finds himself behind the IG-2000, caught in a barrage of fire from the Slave I; Fett is forced into hiding while IG-88D managed to limp off to Ord Mantell to search for spare parts for his ship in the planet's Scraplands.
On Executor, Vader tests his injured hand with an ASP-series droid while briefing Jix about his foresight that Luke will approach Jabba to rescue Han; Jix is supposed to join Jabba's gang and try to capture Luke, and ensuring his survival. Finally, Vader concludes his meeting and arrangements with Xizor.
Battle of Gall
When Lando Calrissian learns from Dash that Fett is on Gall, he meets Luke and Leia on Tatooine. They depart for Gall, where they meet up with Rogue Squadron and Dash. Meanwhile, the bounty hunters Bossk and Zuckuss attempt to join Boba and work together in order to share the bounty of Han, but he firmly refuses and shoots a sniper placed to shoot him, then his system warns him that Slave I has been breached by 4-LOM and two other bounty hunters.
Dash Rendar, with Outrider, leads Leia on the Millennium Falcon with Lando, Chewbacca, R2-D2, and C-3PO to the Slave I through the Grand Trench on Gall, while Rogue Squadron becomes entangled in a space battle against the dayside Star Destroyer. The Falcon reaches the spaceport, though Dash decides to leave since he was paid "only to guide, not shoot".
The Rogues' luck could not last. Another wave of TIEs approached and a second Star Destroyer joined the battle. They decide to cut and run, preparing for a mock hyperspace jump. Plotting a course towards their base on the moon of Kile, Wes Janson's X-wing fires on Luke; his astromech droid had taken control of his ship, and Luke was forced to disable his fellow pilot's fighter.
Boba notices the Falcon approaching and lifts off. The Falcon was badly damaged and withdraws too; the mission had failed.
Eventually Luke finds that Janson's droid had been programmed by a technician to kill him; the technician is shot by Wedge and discovered that she was paid by Vader (actually by Guri). Leia decides to make contact to an underground organization in the hopes of finding out who is responsible. Unfortunately she decides to make contact with the Black Sun, unaware that Xizor is the one who wants Luke dead. Leia also asks Luke to go to Tatooine after Fett not knowing that Xizor expects so; she also secretly hires Rendar to follow and protect him.
Gizz's gang
Big Gizz, while on the town with his buds, is challenged by a mysterious stranger, Jix, in Mos Eisley. When Jix steals Spiker's swoop, Gizz is impressed with his willingness to cheat. Jabba just got a transmission that interfered with Jix's instructions to ensure Luke's survival: that Luke is there, and he is more useful dead. After a discussion in Chalmun's Spaceport Cantina that Dash overhears, Jix and the gang race over to kill Luke.
At Ben Kenobi's hut, Luke tests the new lightsaber he has constructed according to the instructions from a book he found inside. Once the swoop bikers arrive, Luke deflects several blaster bolts before he slashes aside one of the riders and steals a bike within the twists and turns of Beggar's Canyon with Dash coming behind. When Spiker gets a clear shot at Luke, Jix rams his swoop into Spiker's to keep Luke alive. Although Jix breaks a leg in the crash, Spiker is nearly dead. Gizz falls from his bike and levels his rifle at Luke; he's struck in the skull with a rock by Jix.
Fett reclaims the Slave I
Meanwhile Fett hides in an asteroid field when 4-LOM resumes operation. Before Fett disables him once more, Bossk picks up 4-LOM's signal and finds Slave I stranded. Zuckuss and his team board the ship and apprehend Fett attempting to capture the carbonite slab. Furlag leads Fett to his cell but Fett opens a trapdoor under his feet. He keeps Zuckuss alive to communicate with Bossk and sends the shuttle back to him; when Bossk looks inside he sees his fellows dead, along with a detonation device, when Fett jumps to hyperspace.
As Xizor suggests to the Emperor, Bothan spies discover that the plans are to be sent in a small computer onboard a fertilizer freighter, the Suprosa, en route to their home planet Bothawui.
Intercepting the Suprosa
The Bothans send a message droid to Tatooine for Leia, asking her to come to Bothawui, which is received by Luke and Dash who take up the challenge. Along with a fleet of volunteer Bothans including Koth Melan, they intercept the Suprosa as it exits hyperspace.
Luke being captured
Koth Melan and Bothan technicians decode the Death Star plans on Kothlis when a Barabel bounty hunter raid, led by Skahtul, captures Skywalker and kills Melan. It is revealed to Luke that there are two rewards on his head, as he is wanted alive and dead. Unknown to him, it is Vader who wants him alive and Xizor who wants him dead.
After much discussion, Leia agrees to go to Coruscant with Guri in the Stinger, taking Chewbacca with her. To allow the two to make it onto Coruscant without being identified, Guri helps them into disguises. Leia takes the guise of the Ubese bounty hunter Boushh, and Chewbacca is disguised as Snoova.
For a time, Luke meditates and concentrates. After he gains much confidence with the Force, he influences the mind of his cell guard. Luke gets the guard to lock himself in the cell and take a nap, while Luke exits and then proceeds to increase his skills in the Force as he makes his way out of the stronghold. Lando, with information from Dash, makes his entrance and rescues Luke, and they depart from Kothlis on the Millennium Falcon for Tatooine, and in a hurry, as the Executor has just arrived.
Darth Vader aboard the Executor, is sent to Kothlis to collect Skywalker (as well as to make it appear as if the Empire was genuinely concerned with the loss of the plans); the plans managed to reach the Razor over the planet. Then Vader finds Skywalker gone and learns from Skahtul that someone wants Luke dead.
"Boushh" and "Snoova" on Coruscant
Xizor hosts Leia and Chewbacca at Black Sun, then provides them each with appropriate commodities. After an intense seductive experience with Xizor, Leia is reinforced by Chewbacca, eventually retakes control of herself, and knees Xizor between the legs. He is outraged, and sends her back to her room, while Chewie is intentionally let to 'escape' (although not so easy) hoping that he would lead Luke to rescue Leia; and into Xizor's hands.
On Tatooine, Jix cleverly gets past security and makes contact with Vader on the Executor in order to inform him of the swoop bike incident with Luke and learns that Jabba, too, had a bounty for Luke dead, put by someone who used Vader's name.
Luke, Dash, Lando receive a message from Chewie and head for Coruscant where they meet; Chewbacca stealthily make their way through the sewers of Black Sun in order to enter Xizor's palace. Using the Force, Luke and his thoughts inform Leia that he and the group are close by and will soon rescue her from Xizor. After much blasterfire with security guards with Luke integrating his increasingly advanced lightsaber skills, the group finds Leia and begins to lead her out of the palace.
They enter a hallway with Xizor, Guri, and several more of his aides, and a battle soon commences wherein Xizor and Guri are impressed with Luke's skills as a Jedi. Luke and Lando soon threaten Xizor with thermal detonators that they send down the garbage chute, causing everyone to frantically panic and scatter out of Xizor's palace.
The Millennium Falcon, being driven by R2-D2 and C-3PO, wildly careens toward Luke and company, allowing them to escape onto the vessel above Coruscant.
Xizor boards his skyhook, then sends four of his own starfighters at the Rebels, with Dash defending them with flak from the laser turrets of the Outrider. The X-wing starfighters of Rogue Squadron soon join in, along with many TIE fighters, and a big space battle commences.
Vader, via hologram on the Executor over Coruscant, confronts Xizor. Vader warned Xizor to stay away from Luke, but he willfully disobeyed those orders, and he thus orders the Imperial fleet to destroy Xizor's skyhook.
There is a great explosion wherein the Outrider is thought to be destroyed when Dash actually makes a jump to hyperspace at the last moment, as he is convinced that his experiences with the Rebels have been too dangerous while there is too much money to be made elsewhere.
Fett delivers Solo to Jabba
On Tatooine, Fett fools the stalking bounty hunters with a disguised Zuckuss and a covered up 4-LOM that would seem to be himself and a carbonite block speeding away from the Slave I. The real Fett gives the actual carbonite block of Han to Jabba, and he receives his payment. Meanwhile, Luke, Leia, Lando, Chewbacca, R2-D2 and C-3PO prepare to rescue Han from Jabba the Hutt.
For the project, Ryder Windham chose newcomer Kilian Plunkett and veteran writer John Wagner, who had already worked on the Boba Fett series; Windham admired Wagner's work, especially his Batman/Judge Dredd: Judgment on Gotham crossover, and his ability to stage suspense and action scenes. Windham frequently communicated with Steve Perry to ensure consistency with the novelization.
Although Boba Fett is almost unseen in the Shadows novel, a big part of the comic adaptation focuses on Fett's actions. Windham had in mind the short story A Barve Like That, showing the encounter between Fett and IG-88, with the comic showing also its aftermath; with Slave I damaged and Fett trying to deal with his rivals, the Rebels, and Imperials (although the latter are not involved in the final version). Wagner divided Steve Perry's original outline into the story arcs for each issue, and also was informed by continuity editor Allan Kausch's timeline flowchart showing events and actions of each character, provided to each project participant.
Plunkett was so excited working for a Star Wars project that initially he faced brainlocks in his attempt to fit all explosions, angles and "cool things" he could think of in every page; he decided there was no need to fill a page of the swoop bike chase scene with everything, as the scene meant to take place in a dozen pages. Plunkett also kept in touch with Windham to ensure that original characters, objects, and locations were faithful to their other iterations; for the Battle of Gall, Windham sent him what LucasArts had already designed as the planet Gall. Even so, there are some inconsistencies, such as Falleen's Fist, which appears differently in the comic.
Plunkett had almost no contact with Wagner during the creation, as he found his script notes clear enough. The collabolators eventually met and talked first time at the San Diego Comic-Con 1995.
As part of a cross-media promotion for Shadows of the Empire, Kenner released two abridged comic reprint issues of Dark Horse's Shadows of the Empire series within its Shadows of the Empire toy line.
The 1996 Topps Star Wars: Shadows of the Empire collection cards 89-94 feature artwork by Greg Hildebrandt and Tim Hildebrandt inspired from Boba Fett's actions in the comic.
Metallic Impressions released 36,000 1997 Metallic Impressions Star Wars: Shadows of the Empire sets of six collectible metallic cards; each one displays cover artwork by Christopher Moeller, a panel from that issue along with a title and a summary. The proposed titles of each chapter are: Xizor's Plan Revealed, Rescue Attempt on Gall, Wanted: Luke Skywalker, Leia Meets Xizor, The Trap is Set and Han Delivered.