Star Wars: Empire: The Wrong Side of the War, a narrative spanning issues 36 through 40, marked the culmination of the ten-part story arc in the comic book series Star Wars: Empire.
Following the devastating events on Jabiim, where the Empire decimated the local population, Imperial Lieutenant Janek Sunber finds himself reassigned to the seemingly tranquil prison facility on Kalist VI. Unbeknownst to the Empire, the Rebels are targeting Kalist Base, drawn by its valuable fuel reserves and the presence of a high-profile prisoner—a fellow Rebel who has already garnered Darth Vader's attention.
Unaware of the events unfolding, Sunber is destined to cross paths with a former comrade now aligned with the Rebels, leading him to question which side truly represents the moral high ground in this conflict.
Roughly eight months following the Battle of Yavin, Lieutenant Janek Sunber is engaged in the final stages of suppressing the remaining resistance on Jabiim. Despite determined opposition, Imperial stormtroopers overwhelm the last Jabiimi stronghold. The captured Jabiimi are then escorted to a waiting assault ship for relocation to the Imperial base situated on Kalist VI. Sunber, accompanied by his clone stormtroopers, is also aboard, anticipating a peaceful assignment to garrison duties.
As the transport emerges from hyperspace, it unexpectedly encounters a skirmish between a Rebel X-wing squadron and an Imperial fuel tanker struggling to stay afloat. The arrival of the assault ship, coupled with TIE fighters dispatched from Kalist, forces the Rebels to retreat.
Upon the transport's arrival at the base, the prisoners are disembarked, along with a significant asset, Rebel analyst Jorin Sol. Simultaneously, the fuel tanker Nuna's Twins docks on a platform atop the base. The vessel's Captain Harran receives a warm, yet cautious, welcome from the garrison commander, General Noils, who assures them of every courtesy once the Rebel threat is neutralized. Following his departure, Harran confides in his fellow Imperial imposters, Luke Skywalker and Deena Shan, expressing relief that their infiltration appears successful.
Meanwhile, Lieutenant Zuud, an officer of Imperial Intelligence, subjects Jorin Sol to torture, calmly stating her desire to discover the extent of his loyalty. The stormtroopers guarding Nuna's Twins are taken aback by the emergence of additional troops from the tanker, only to be swiftly eliminated by their 'comrades', who are revealed as Rebel infiltrators in disguise. Harran swiftly coordinates the team, dispatching some to create distractions while others locate Sol and prepare the tanker to be filled with fuel, a critical resource for the rebellion.
Sunber, having begun settling into his new wardroom, is promptly confronted by Lieutenant Clynn, the resident bully, who insists that the wardroom rightfully belongs to him. A brief altercation ensues, during which Sunber easily overpowers Clynn despite his superior size. Captain Kale Roshuir intervenes, assigning the pair joint extra duties as punishment.
In the base's command center, Captain Harran, Luke, and Deena meet with General Noils and Captain Roshuir. They discuss the recent Rebel assault that damaged Nuna's Twins and previously destroyed its escort frigate. Deena volunteers to aid Roshuir in pinpointing the location of the Rebel base believed to have launched the attack.
Deep within the base, Lieutenant Clynn conducts Sunber on a tour, showcasing the prisoners forced into slave labor—an unsettling sight for Sunber—and dismissing them as individuals who "...gambled on the Rebellion and lost—big". Above them, rebel infiltrators Basso and Able, disguised as stormtroopers, are strategically placing explosives. Basso is also deeply disturbed by the use of slave labor, urging that Captain Harran be informed.
Having been dismissed from Harran and Noils' presence, Luke proceeds to monitor the covert fuel theft from the base's reserves, overseen by R2-D2. Clynn leads Sunber to the prisoners' mess hall, where he seizes a female laborer. When her partner attempts to intervene, Clynn assaults him, knocking him to the ground. Appalled, yet resolute, Sunber follows Clynn and the female prisoner to a secluded room, where he discerns the officer's intentions and demands that he release the prisoner—at blaster-point. Enraged, Clynn warns Sunber that he has "...no idea of the trouble headed your way" and departs.
Aboard Nuna's Twins, Luke and Basso persuade Harran to attempt to aid the prisoners in escaping. Meanwhile, Deena lies in Captain Roshuir's bed as he dresses, informing her that he has been chosen to lead the assault on the suspected Rebel base on Thila. He suggests they further discuss their relationship upon his return, leaving a distraught Deena contemplating "What have I done?"
The commotion of the base's stormtrooper companies preparing for departure awakens Sunber, but Roshuir curtly informs him that he is confined to base for brandishing a weapon at Clynn. His objections are dismissed, and he is informed that he will soon face a tribunal.
While observing the departure of the Imperial assault force from a landing pad with Deena, Luke is stunned by the appearance of Sunber – his old friend from Tatooine, nicknamed "Tank". Deena excuses herself, allowing them to reminisce. Sunber voices his doubts about the Empire to Luke, who challenges his adherence to duty over morality.
In the interrogation chamber, Zuud relentlessly pressures a weary and tormented Sol for an answer to her demands. Aboard Nuna's Twins, trooper Able argues against rescuing the prisoners, but Harran overrules him.
On Thila, Roshuir oversees the entry of his stormtroopers, led by Lieutenant Clynn, into the remnants of what appears to be an abandoned Rebel base. As the squads disperse to search the base, a booby trap is triggered, resulting in the deaths of Clynn and most of the troops, although Roshuir and the landing craft on the surface survive. Devastated by the loss of his men, Roshuir realizes that Shan has betrayed him.
On Kalist VI, the Rebel infiltration team learns that Jorin Sol is being prepared for transport to Coruscant, making this their final opportunity to rescue him. Harran instructs Deena to remain aboard Nuna's Twins and prepare it for liftoff. Elsewhere in the base, Mouse is apprehended by stormtroopers while planting explosives, but temporarily evades them by removing his helmet, catching them off guard.
As Luke attempts to persuade a shocked Sunber to join the rebellion, Mouse is ultimately captured and killed by the stormtroopers—just as he activates the explosives. Sunber receives an alert from the base command center that rebel agents have infiltrated the facility, coinciding with the detonation of the explosives. Sunber abruptly realizes that his old friend is a rebel and reaches for his blaster pistol, but Luke knocks him unconscious before he can draw it.
The stormtroopers and officer escorting Jorin Sol to his transport are ambushed and killed by the disguised Rebel infiltration team, while Luke convinces the prisoners to escape with his assistance. Deena, standing at the ramp of Nuna's Twins, is seized by Captain Roshuir, who has just returned from Thila. However, before he can shoot her, Harran tackles him, knocking him out. Simultaneously, Rebel bombers are attacking the base.
Sunber navigates through the debris-strewn base and discovers the bodies of his stormtroopers, slain by Luke, reinforcing his belief that duty is all he has left. As Luke supervises the boarding of the prisoners onto the assault ship docked at the base, Janek confronts him at blaster-point. Appealing to Sunber's sense of morality, Luke nearly sways him when Jorin Sol and the rebels escorting him appear. Enraged by what he perceives as Luke's deception—that the rescue of the prisoners is merely a facade for the retrieval of a 'Rebel spy'—Sunber fires at Sol, but Luke deflects the blast back at him with his lightsaber. Wounded, he refuses to accompany Luke, declaring "I can't do it Luke. You're on the wrong side of the war. Biggs would have agreed with me". He is left speechless when Luke reveals that Biggs Darklighter had, in fact, been a rebel.
Red Squadron escorts the assault ship—newly christened Skywalker—and Nuna's Twins away from the base, leaving an enraged and powerless Captain Roshuir shaking his fists.
As Sunber observes this, Zuud arrives with another officer and some stormtroopers, and to Sunber's bewilderment, appears to express satisfaction at Sol's escape. Sunber is further perplexed by the swift arrival of Imperial reinforcements, including a Star Destroyer, almost as if the attack had been anticipated...