The tale begins above the remote world of Shumari. A massive force of Star Destroyers are bombarding the planet, reducing its surface to rubble. On the surface, a group of stormtroopers are in battle with a large group of Jedi with heavy casualties on both sides. The attack is interrupted by the sudden arrival of Darth Vader, who has arrived to complete the destruction. Several of the remaining Jedi charge Vader, attempting to cut him down, but they are no match for the Dark Lord of the Sith who easily dispatches with his attackers. The leader of the Jedi, appalled by the deaths of his allies, steps forward, claiming that Vader will pay for the slaughter. Vader begins to choke the man with the Force, but he is able to resist, launching himself at the Sith Lord. However, Vader is prepared for the attack, and he stabs the man through the chest. Unseen by Vader, a young Jedi Padawan, Tao, approaches the slaughter. The Jedi leader, with his dying words, pleads with Tao not to attack, asking that Tao live through this encounter. Vader turns to face Tao, who, although badly injured, has ignited his lightsaber. Vader sees the hate in Tao's eyes and ponders what to do with the young Jedi…
Sometime later, on Yavin 4, Luke Skywalker is walking through the hangar bay of the Great Temple. He finds Han Solo and confronts him about leaving to avoid the upcoming battle. Han shrugs off the criticism, and Luke leaves, but not before Han wishes him good luck. The X-wing starfighters of Red Squadron begin their attack on the Death Star. Darth Vader enters the battle in his TIE Advanced x1, shooting down the enemy pilots. Luke and his wingmates, Biggs Darklighter and Wedge Antilles, begin their Trench Run. They are pursued by Vader, who kills Biggs and forces Wedge to withdraw. Before Vader can shoot down Luke, he is interrupted by the arrival of the Millennium Falcon, piloted by Han. The smuggler shoots down one of Vader's wingmates, causing the other one to become distracted and collide with Vader's starfighter. Vader and his spacecraft spin off into space as Luke destroys the Death Star. As the Rebels celebrate their victory, Vader is coasting through space, where he vows revenge on the victorious Rebel pilot.
Sometime later, a fleet of Star Destroyers is approaching Coruscant. The citizens of the planet have heard rumors that the Rebels have won an important victory. Although worried about the possible danger the Rebels might pose, the citizens reassure themselves, claiming that they are safe as long as the Emperor is with them. Amidst cheers for the longevity of the Empire, Darth Vader arrives on the planet where he is greeted by several stormtroopers and a scarfaced Imperial officer. Vader dismisses the officer's greeting, telling him to use any means necessary to uncover the identity of the Rebel pilot who destroyed the Death Star. Vader makes his way to the Imperial Palace to speak with his master, Darth Sidious. In the Emperor's throne room, Vader is greeted by his master, who rebukes him for his failure at Yavin 4. The Emperor claims that he can see right through Vader, witnessing his inner thoughts about his past. After reminding Vader that he is his tool, Palpatine dismisses him.
Vader makes his way back to his tower and retires to his meditation chamber. As Vader begins to meditate about the identity of the Rebel pilot at Yavin, he is interrupted by Tao. Tao claims to Vader that he senses a new feeling inside of his master, that of happiness. Vader is amused by Tao's belief, and he tells the boy to attack him. Tao strikes at Vader, but the Dark Lord easily deflects his attacks. Vader claims that Tao is not attacking with enough ferocity, and he orders his student to use his anger and hate him. Tao is unable to harness his anger, and he cries out, claiming that he can't use his hate.
Vader yells at Tao, claiming that his student should have no problem hating him. After all, it was him who destroyed his home planet, killed his parents, and took everything away from him. Despite Tao's protests, Vader claims that he cannot accept weakness. Tao vows that he will become strong, and Vader, satisfied, says that the lesson is over. Vader leaves his tower and boards a Lambda-class T-4a shuttle. Vader travels to a Star Destroyer to oversee the launching of several shuttles. During the operation, he is contacted by the scarfaced Imperial officer who gives him a holoprojector containing the name of the Rebel pilot. Vader activates the hologram to see the face of Luke Skywalker. Vader recalls the face of the young man on the Death Star who had fired at him after he had killed Obi-Wan Kenobi. Vader concludes that Luke must be the child he had fathered with Padmé, who he had thought dead. Elated by the thought of his son, Vader vows to hunt down and be reunited with his child.
Back on Coruscant, Vader is back in his meditation chamber when he is approached by Tao. Tao claims that he is ready to continue his training, but Vader tells the boy that he has no more time for him anymore. Tao is distraught, asking why the Sith Lord spared him in the first place. Vader tells Tao to go wherever he likes but that he will have nothing more to do with him. Sometime later, the Coruscant populace is looking up as a massive warship begins to cast a shadow across the city. Vader is standing with Palpatine on a balcony, and he presents the ship, the Executor, to Vader as a gift. Vader takes the ship into space where he oversees the release of probe droids throughout the galaxy. As Vader ponders hiding the existence of his son from Palpatine, he is bumped from behind by a defective R2 unit. Vader tells the scarfaced officer to dispose of the droid, but before he can, a hologram projects from the R2 unit. Palpatine has discovered Tao, and two Royal guardsmen present the young boy to Vader. Palpatine orders his apprentice to strike down Tao, and Vader eventually obeys, running his lightsaber through the boy. Palpatine is pleased by the show of loyalty, and the hologram dissipates.
Vader looks down at his badly injured student, who is remarkably still alive. Vader decides to return Tao to his home planet to die. Tao thanks his master for the gesture of kindness and claims that he can sense the good in him. As Vader carries the boy's body across the destroyed terrain of the world, he senses a presence following him. A Tusken Raider, a survivor of Anakin Skywalker's mission to Tatooine, has come to avenge his slaughtered brethren. The Tusken has learned Basic and studied how Vader fights. With his own lightsabers, the Tusken attacks Vader, who becomes awed by the sense of rage contained within the being. Before the Tusken can attack Vader further, Tao summons the strength to rise in defense of his master. Tao kills the Tusken Raider, but his injuries have taken their toll. With Tao's final words, he asks that Vader give up his anger.
Vader takes Tao's dead body and buries it, carving a headstone with Tao's name before he leaves the planet. Vader travels to Tatooine and visits the Lars homestead. Staring out at the twin suns of the planet, Vader thinks about his son, claiming that he is the new hope in his life. Sometime later, at the Battle of Hoth, Luke is crawling away from the AT-AT that he has destroyed. Han and Chewbacca are attempting to escape Echo Base, when Darth Vader enters the base with a squad of Snowtroopers. As the troopers overrun the base, Vader is reassured, and he tells himself that his destined vengeance begins now.
Originally published in Japan, stories from Star Wars Manga were considered to be of "fuzzy" continuity by Lucasfilm. Since then, they have been republished in English in the United Kingdom under Infinities label, which established the material in them as non-canonical.
Author Daniel Wallace stated definitively in the article We Need to Talk About Jar Jar, written for Star Wars Insider 131 in February 2012, that the stories included in the Star Wars Manga: Black comic trade paperback are non-canon.
The planet Shumari has been later referenced in The Essential Atlas, which included the Shumari system in its appendix. However, according to Jason Fry, "its inclusion shouldn't be taken as a statement of canonicity for anything except the geography." The Blog Barely Tolerable: Alien Henchmen of the Empire Part 2 also briefly alluded to this manga in the ending of KkH'Oar'Rrhr's section, specifically Vader's encounter with the sole-surviving member of the Tusken Raider village he had wiped out. Similarly, Tao ended up mentioned in Ennix Devian's section on the second part of the blog "The Imperial Warlords: Despoilers of an Empire" as one of Vader's secret apprentices alongside Galen Marek (Starkiller) as well as being one of the few people alongside Devian and Marek to have the honor of facing Noghri Death Commandos during training. Because of this, the manga is considered ambiguously canon.
This issue conflicts somewhat with the previous backstory concerning Darth Vader's discovery of the identity of the pilot who destroyed the Death Star. Marvel Star Wars first showed Vader discovering the name on the Rebel refueling station in Star Wars (1977) 35. A later comic, Vader's Quest, built on this story somewhat by having Vader discover only the last name on Centares as well. However, Perfect Evil, shows Vader receiving a report on the name from one of his Imperial officers. Since it is not specified when this report occurs, it may be possible that the report was simply a follow-up to the discovery of the name on Centares.
In the second part of the comic, when Vader claims to Tao that he killed his parents, a flashback image shows the death of the bearded Human Jedi from the beginning of the comic. This may mean that the Jedi is in fact Tao's father. This may be supported by Tao's anger at the beginning of the comic when he witnesses the death of the man and the Jedi's final words to Tao.
After Vader makes Tao into his student, Tao takes on the appearance of a younger Anakin Skywalker. Along with the same outfit, Tao's right arm is fitted with a cybernetic replacement.
When Vader returns to Tatooine near the end of the comic, he claims that Luke is a new hope in his life, referencing the title of Star Wars: Episode IV A New Hope.
The gravestone of Tao is written in Aurebesh. The hologram of Luke Skywalker contains his name and the caption "REBEL ALLIANCE PILOT."