The third and concluding annual issue of the Marvel Star Wars comic book series is titled Star Wars Annual 3: The Apprentice.
Darth Vader is aboard a Star Destroyer, conversing with several Imperial officers. The Dark Lord outlines a strategy to conquer the Belderone system, starting with the planet of Belderone, where the Empire has established a clandestine factory. A Rebel base has been located on the planet Kulthis, and Vader intends to utilize the Empire's presence on Belderone as a launchpad for a devastating assault on Kulthis. General Andrid expresses doubt about Vader's scheme, suggesting it stems from a sentimental attachment, perhaps from his time as a Jedi Knight. Vader responds with a stern warning, advising the general not to test him, lest he face the Dark Lord's fury.
On Belderone, a young man named Flint is running through the city streets, calling out for his friend Barney. A Rebel vessel has touched down at the spaceport, and Flint is eager to see it and its passengers. Barney is less enthusiastic, but Flint persuades him to join. As the two friends head to the spaceport, Flint's mother, Zana cautions Flint not to be tardy for his shift at the factory, as the Imperial supervisors are very strict regarding citizens missing their mandatory work. Flint assures her he'll be back on time, and the two young men rush to the spaceport, arriving just as the Rebel group is disembarking. The Rebel party consists of Luke Skywalker, Lando Calrissian, Leia Organa, Chewbacca, R2-D2, and C-3PO, who immediately engage with the gathered citizens, seeking confirmation of rumors about an Imperial operation on the planet. Upon mentioning their origin from Kulthis, the crowd quickly disperses, as no one desires association with anyone from a Rebel-sympathizing world. However, Flint and Barney step forward, having noticed Skywalker's lightsaber. Flint's father had also been a Jedi Knight, and he questions Skywalker about whether his father was also a Jedi Knight. Luke, having recently learned that Darth Vader is his father, fabricates a story, claiming his father was merely a "navigator on a spice freighter". Despite this, Flint remains excited by the presence of outsiders and decides to escort them into the city, leading them towards his mother's tavern. As the Rebels are ushered inside, a tavern employee recognizes them and alerts General Andrid.
Andrid decides to bypass Darth Vader and handle the situation independently. He contacts three assassins stationed on the planet and provides them with the Rebels' location. However, the attack is unsuccessful. Skywalker anticipates the impending assault using the Force, and the Rebels swiftly eliminate two of the assassins. The group attempts to apprehend the third assassin, but he immediately takes his own life. Skywalker's remarkable reflexes during the shootout confirm to Flint that Skywalker is indeed a Jedi, convinced that only the Force could enable such skill. The ambush confirms for the Rebels that a significant operation is underway on Belderone, aimed at destroying the Rebel base on Kulthis. While Lando and Leia opt to remain on Belderone, Chewbacca and Luke return to Kulthis aboard the Millennium Falcon to warn the Rebels. A squadron of single-person craft had been assembled before the Rebels' arrival on Belderone, and the group hopes to strike the Imperials before they launch their attack on Kulthis. As the Millennium Falcon departs, Flint and Barney contact the Rebels, deciding to reveal the factory and its construction activities.
Simultaneously, back in space, Darth Vader receives news of General Andrid's ill-advised attack. Realizing that the Rebels are now aware of the Empire's presence, he uses Force Chokes to kill the man, and orders the immediate commencement of the Imperial attack, placing Colonel Maldrod in command. Back on Belderone, the Rebels reach the factory only to witness several AT-AT walkers emerging from the underground structure. The Imperials intend to proceed directly through the nearby town and rendezvous with several Imperial bulk cruisers that will transport them to Kulthis. Leia and Lando infiltrate the factory, while Flint and Barney commandeer a landspeeder and race towards the town, hoping to alert the populace to the impending walker assault. However, upon reaching the town, Flint accidentally crashes the speeder, rendering both of them unconscious. With the AT-ATs threatening to devastate the town, Skywalker arrives with the squadrons from Kulthis. A fierce battle erupts near the city, and one of the AT-ATs begins to wreak havoc, destroying everything in its path. The Rebels ultimately succeed in destroying all the AT-ATs and the AT-AT factory with the assistance of Leia and Lando, who had managed to commandeer one of the walkers.
The following morning, Flint regains consciousness to find his town utterly destroyed. He spots Barney lying nearby, still unconscious, and presumes him dead. Flint rushes to his mother's tavern and begins searching through the debris. Amidst the wreckage, he discovers his mother's lifeless body, filling him with immense sorrow. As Flint grieves over the devastation, he is encountered by Darth Vader, who expresses sympathy for his situation. Vader invites Flint to join the Empire, promising to provide him with special training to make him "someone who matters very much." Meanwhile, back with the Rebels, Barney has received medical attention and has decided to join the Rebellion, as his entire family perished during the battle. Leia attempts to apologize for the destruction of the city, but Barney assures her that he knows the Rebels are not to blame.
Back with the Imperials, Flint has donned his stormtrooper armor. After casting one last glance at a photograph of his former life with his mother, he puts on his helmet and boards an Imperial transport vessel. Darth Vader watches approvingly as the rest of his stormtroopers board the Imperial ship.
The placement of this comic in the timeline, as indicated in the Marvel Star Wars collection, Star Wars: A Long Time Ago... Volume 5: Fool's Bounty, is between Star Wars 78 and Star Wars 79. However, this placement is likely due to the publication date, as Luke, Lando, Leia, Chewbacca, R2, and 3PO are all present together in this issue, while they are divided into two groups in issues 78 and 79.
The AT-ATs depicted in this issue appear to be significantly larger than typical AT-ATs. This is evident when an X-wing starfighter is able to land on top of one of the vehicles without any overhang. While this discrepancy may simply be attributed to artistic license, Abel G. Peña has proposed in an online essay, "The State of the Galactic Civil War," that these may have been experimental walkers.
It is noteworthy that Darth Vader recruits Flint into the Empire after discovering the young man mourning his deceased mother. Although purely coincidental, given that Star Wars: Episode II Attack of the Clones was released nearly twenty years after this comic, Vader's loss of his own mother to Tusken Raiders bears a striking resemblance to Flint's experience. Particularly his desperate attempt to reach his mother's safety, only to arrive too late to save her.