Doctor Boynton is a robotics engineer struggling for a breakthrough, while his son Toby longs for his affection. One night, a shady criminal, Skunk Kusai, visits his home and offers Dr. Boynton a new circuit known as the Omega Factor, which would allow robots to become far more human-like, to the point of defying all Laws of Robotics. Boynton angrily throws him out of his home. Toby, having overheard their conversation, suggests to his father that he design a new robot that resembles a human boy. Boynton is inspired by this, and creates a new template for this design. However, he neglects his promise to spend time with Toby at an amusement park, hurting Toby's feelings. As Toby leaves the park, he is caught in a traffic collision and is horribly injured, and dies from his wounds in the hospital; before this, he has his father promise him to make the robot in his image and treat it like his own. Overcome with grief, Boynton completes the project, christening the new robot after his deceased son, and brings him to life. However, Skunk has copied the template designs as well, and takes them to a scientist named Walpurgis, who builds a robot he names Atlas. Boynton takes the robot Toby home, teaching him about life and how to live like a little boy. However, some time later Toby becomes paralyzed, his eyes blinking red, and disappears from Boynton's home. Boynton and his colleagues track Toby down using a robot tank, but the tank suddenly goes berserk with them inside, causing Toby to rush to save his father and his colleagues. Little do they realize that Toby's behavior was caused when Atlas was activated; the two robots had "called" one another. Later, in the hospital, Boynton tells Toby that he is very proud of him, but since he was no longer a secret, the two would have to leave the country for a while. Atlas and Walpurgis' robot maid, Livian, discuss his purpose, with Atlas uncertain of what lies ahead for him.

Dr. Boynton and Toby depart on an ocean liner for America, but Toby is unintentionally destructive, as he doesn't realize his own strength at times. Frustrated, Dr. Boynton has him stay in their cabin while he heads for dinner. However, a couple of guests want to meet Toby, so he has no choice but to bring him along. During the dinner, the guests realize that Toby is a robot, and even though he means no harm, manages to ruin the dinner by tipping the table over, causing a huge mess. Angrily, Boynton rejects Toby on the spot, declaring that he's just a robot and that he has no son. Meanwhile, Skunk Kusai has taken to educating Atlas in crime, teaching him how to rob armored trucks. Atlas, however, destroys the trucks before robbing them. Skunk then tries to teach him how to rob a supermarket, but Atlas, instead of stealing money, makes off with receipts instead. Frustrated with his incompetence, Skunk tells Walpurgis that Atlas is a fool and the Omega Factor has done nothing for him, but Walpurgis counters that Atlas is becoming more humanlike, and mistakes are a human factor in learning. Atlas, meanwhile, is consoled by Livian, who begs him not to follow a life of crime, but Atlas insists that he become more human to impress Walpurgis. Livian tells Atlas that a man must not harm those weaker than he, and even though they are robots, they also identify by gender. Atlas asks if Livian can be like his mother, as she is the only one who truly makes him happy. However, Skunk interrupts their talk to take Atlas on a mission. As Toby considers what Boynton said to him, he is approached by a shady circus owner, Hamegg, who asks if he would like to join the circus now that he had been disowned by Boynton. He takes Toby with him and coerces him into signing a contract, declaring Toby Hamegg's property. Meanwhile, Skunk tells Atlas that he plans to sink the ocean liner and have Atlas go in and steal a haul of gold bars on board. His plan is to create a field of icebergs in the path of the ship to cause it to crash. Setting off explosives, he creates a large flow of icebergs, but Toby manages to destroy the icebergs by breaking them up, saving the ship. He encounters Atlas, who attacks him and nearly destroys him until he recalls Livian's words. In a show of mercy, Atlas leaves Toby on the ship's deck, where he hears Boynton, who feels remorse for what he has done, calling out in desperation for him. However, he is found by Hamegg first, who grabs him and stuffs him in a crate. Atlas returns to Walpurgis' castle, where he finds that Walpurgis has dismantled Livian as punishment for her accidentally destroying a gargoyle sculpture. In a fit of rage, he attacks Walpurgis, who escapes by car. Atlas chases him, and even though he is severely damaged by missiles from the car, manages to catch him and run him off the road, apparently killing Walpurgis. Atlas returns to the lab and uses Walpurgis' equipment to begin rebuilding his body.

Combines parts of episodes 1 and 2.

Toby is enslaved by a robot circus owner and is forced into manual labor, but befriends a young circus worker named Kathy. When Boynton's associate, Professor Elefun, comes to fetch him but the ringmaster refuses to surrender him, Kathy does the best she can to save the boy robot. It is during this episode that Toby receives his new name, "Astro Boy", and his characteristic red boots.

Rescued from the circus by Dr. Elefun, Astro Boy struggles with the bullying from classmates for being a robot.

In Astro's second encounter with Atlas, he stops Atlas's scheme of enslaving humanity by a series of technological thefts, one of which involves the proposed robotic mother and father for Astro.

Note: This episode's title does not make sense in the context of the English dub as Atlas had not made an appearance in the series yet due to the combining of episodes 1 and 2. Astro's encounter with Atlas also doesn’t make sense as Astro recalls the fight they had on the iceberg, refers to Atlas by name and recognises him despite having not been shown meeting. There is also no proper explanation for Atlas’ change in appearance in the flashbacks and the present time. It could be argued that the events of Astro vs Atlas that were cut out still happened, albeit off screen.

Astro Boy and Dr. Elefun are led to a animatronic fairytale theme park when a escaped swan/princess crash lands in their yard and tells them of their abusive indentured plight.

The premature activation of a powerful Frankenstein robot is further exacerbated when Skunk convinces the robot to aid in his crime spree. The robotic crime wave leads to the deactivation of almost all robots in the city and briefly, even Astroboy.

A red cat becomes the only clue to the mystery of disappearing children whose parents are involved in the development of the city's last natural and undeveloped area.

While exploring the desertification of a forest, Astro Boy confronts Atlas for being cause but more so his crystal spaceship.

Astro Boy and Dr. Elefun aid a championship racer whose vehicle, the white planet, was destroyed as part of Skunk's plan to win a global race.

Astro Boy and Daddy Walrus are invited to the inauguration of the first robot president and are caught up in the opposition party's plan to stop the ceremony.

A spacecraft crashes to the earth and a robot staggers burning from the wreck. Doctor Elefun contacts Astro, who rescues Goliath from the flames. Goliath is a mining robot from Mars, with his eyes on his chest. His head contains a neutron beam. Elefun has it removed for safety, but it is stolen. Goliath leaves and goes looking for his head, removing and trying on several other robot's heads. Daddy Walrus also searches for the head, discovering it being sold at a criminal auction. Skunk Kazi gasses the crowd and takes the head. he offers to return it to Skunk if he will destroy Astro. However, a tank with the head mounted on it fires on them while they fight and they are buried under rock. Walrus (as Sam Bannister) shoots it out with the criminals at their hideout, but Skunk gets into the tank and uses the neutron beam on the police. Astro dodges the beam and wrecks the tank and Walrus knocks out Skunk. Astro returns the head to Goliath, but the two fight for the head and the beam discharges, annihilating Goliath.

Skunk kidnaps and corrupts a robot capable of invisibility.

In a New Year's celebration, Dr. Elelfun presents Astro's family a younger robot sister Uran. Uran's naïve and precocious demeanor gets her involved with a Pied Piper villain who kidnaps robot children in slavery.

Astro Boy gets involved in a rivalry of scientists who used their robotic creations to one up one another; however, the two robots from the competing camps fall in love.

Astro captains the Second Expedition to Mars, eventually fighting hostile aliens.

Astro Boy gets involved in Skunk's outer space pirating attempt when a classmate is kidnapped.

Astro Boy and classmates are kidnapped by Atlas on school field trip to a comet.

Astro untangles the mystery of balloons modeled after him as they attack the city, and everyone (except Astro's family, Dr. Elefun, and classmates Mindy, Theodore, and Kenneth) thinks Astro is responsible for the making of these balloons.

Astro Boy visits a robot inhabited island where gangsters attempt loot uranium resources by enlisting the help of a robot who can transform into any shape.

The luxury spaceliner Titan is struck by an asteroid. Astro and several others are the last to escape before it explodes. Their lifeboat malfunctions, but they are able to land on the moon, in a crater with an atmosphere. Astro discovers the wreck of a Russian spacecraft from 1990 whose female pilot survived for thirty years, building a robot, Ivan and discovering several large diamonds. The diamonds are meaningless until rescue, when one of the passengers, a ruthless man (Boon Marukubi), decides to take the diamonds. He finds them, but gets left behind. Ivan takes care of him.

A school field trip to a seismology department is interrupted by a robot constantly lying about a impending earthquake.

Astro Boy and mysterious alien woman work together to stop an hostile alien invasion.

A power-hungry Sultan commissions a powerful fighting robot named Pluto (Bruton in the dubs) with 1 million horse power, and sends him to battle 7 of the world's strongest robots: Mont Blanc, Molnar, Brondo, Zeron, Hercules, Photar, and Astro. Bruton manages to easily destroy Mont Blanc by catching him off guard. When he heads to battle Astro, he instead is met by Uran, who tells him Astro won't fight him. Bruton takes Uran hostage to lure Astro into a fight, and goes and destroys Molnar. When Astro catches up to Bruton, the robot wrestler Brondo appears, looking to avenge the death of his friend, Molnar. Bruton returns Uran to Astro, and takes on Brondo; however, he is heavily damaged in the fight. He begs for Astro to activate his summoning beacon to call his master; Astro does so, earning Bruton's gratitude. Later, Astro is contacted by Zeron, who has a warrant for Bruton's arrest. Soon after, Zeron is challenged by Bruton, and nearly gains the upper hand until Bruton rips his body in two. Soon, Dr. Elefun locates the Sultan's palace and flies there, with Astro tailing him. The Sultan holds Dr. Elefun hostage, as a bargaining chip to make Astro fight Bruton. Bruton returns to the palace and encounters Astro, and the two battle until Bruton catches Astro in his hands, and threatens to tear him apart.

Bruton releases Astro, as thanks for helping him before. Astro begs him to reconsider having to fight, but Bruton explains that he cannot, as that was his primary purpose. Bruton goes off to battle Hercules, a powerful Greek Spartan robot. Bruton successfully destroys him, then goes on to battle Photar, a kind, compassionate robot who takes care of orphans. Photar begs Bruton for the chance to say goodbye to his orphans, which he grants. Later, they battle in a terrible storm; as Photar is a solar powered robot, he runs out of energy and is destroyed. The Sultan calls out Astro once again, and has him battle Bruton at a volcanic valley. However, the volcano threatens to erupt and destroy all of the nearby villages and towns unless the power is contained. Astro begins throwing boulders into the volcanic vent to contain the power and begs Bruton for assistance. Bruton initially refuses, but finally has a change of heart and begins assisting Astro, much to the chagrin of the Sultan and the delight of Elefun. The two successfully stop the volcano from erupting, and Astro commends Bruton for his help and tells him that he is a good robot after all. Their victory is cut short, however, when Sultan's scientist, Dr. Abraham, reveals his own secret creation: a super robot named Bora, with a 2 million horsepower engine, and enough destructive force to knock out other robots simply by yelling its name and creating a katabatic wind. Bruton asks Astro to give his regards to Uran, and sacrifices himself to attempt to destroy Bora. However, Bora survives this attempt with nary a scratch, forcing Astro to fight it. He manages to destroy Bora by getting it to attack itself, and getting inside its damaged body and blasting its innards. As Sultan mourns the loss of Bruton, Abraham reveals himself to be a robot; he was Sultan's robotic assistant, and created Bora to prove that brute force alone isn't everything. Astro and Elefun mourn the loss of Bruton, as well as Mont Blanc, Molnar, Brondo, Zeron, Hercules, and Photar, and hope that a future will come where all of man, and all of robots, can live together in peace.

A wild gang of robots rampage through the city, causing havoc and destruction. Meanwhile, Uran is trying to teach Jump how to do tricks, but gets upset when Jump can't perform one of her tricks. Astro explains that Jump isn't the same as a robot, and Uran becomes upset and keeps Jump out of the house. When she finally relents and lets Jump back in from the rain, she gets angry when he shakes himself off all over her toys. Astro scolds her and tells her of the history between him and Jump. That night, the robot gang attacks Astro's house, grabbing Jump and throwing him into a high rise building. The next morning, Astro discovers the footprints from the robot gang in the yard, and Astro's father tells them that the papers reported on the incident, calling the gang "Robot Vikings". Just then, a neighbor comes to the house, bringing a badly injured Jump with her, frightening Uran and Astro. Determined to confront the Robot Vikings for their crimes, Astro wants to head off to find them, but is stopped by his mother, who tells him that Dr. Elefun is not in town to give his consent to fight. Astro's father hires a temporary robot watchdog, and that night, when the Robot Vikings return, it manages to take out several gang members before getting destroyed. Astro intervenes and damages another member, until the entire gang retreats at the sight of a press helicopter. The police inspector calls Astro the next morning and demands he stay in his home. Disguising himself as a dog, Astro sneaks out to search for the Robot Vikings. When he encounters them, he surprises them all by easily besting them in combat, but they attempt to gain the upper hand and combining themselves into a centipede-like tank robot; Astro manages to trounce them. In a last ditch effort, the leader tries spraying Astro with an adhesive, but Astro manages to drag the entire gang across town and electrocute them, but the gang escapes. Later, Astro phones Uran but is scolded instead by his father, who tells him that Uran is at the vet watching over Jump; she felt remorse for her previous treatment of Jump and does not want to see him die. Tracking the Robot Vikings to a cavern, Astro is shocked to find Livian, Atlas's assistant, encased in a glass coffin. The Robot Viking leader attempts to kill Astro by flooding the cavern with lava, but Astro escapes with Livian, while the Robot Vikings die in the lava. Astro encounters Atlas, who is grateful that he saved Livian, and explains that the Robot Vikings were once his soldiers, but were given the Omega Factor, causing them to rebel. Astro berates him for using the Omega Factor so blindly, but Atlas brushes it off, wishing to repay Astro for his help. Astro asks him to make a medicine to help Jump; although puzzled, Atlas complies and delivers the serum to the vet. Jump recovers from his injuries and returns home to Astro and Uran, who now appreciate his presence more than ever.

Uran is watering a growing tulip when a time travel machine arrives from two centuries in the future, crushing down on her tulip. Rock, a time traveling detective, merges from the machine and announces that he is searching for Astro to participate on his adventure, and soon takes him and Uran in the machine, which then travels to the then-present day where the infamous surgeon, Black Jack and his assistant Pinoko are awaiting breakfast. Rock is also picking up Black Jack on his journey, and soon reveals that he is taking him and Astro to 15th century Silverland in order to save the life of Prince Sapphire, who, in a twist of irony, was injured from an earlier excursion to the past by the time traveller; at the same time, Rock was also tracking down a rogue fugitive from another time - Gor, an evil sorcerer who is plotting to usurp the throne from Sapphire and conquer all of Silverland with an army of monsters to do his bidding. The time machine arrives at the kingdom, where Astro recently stops a march of mutated monsters attacking the guard. With the client under his disposal, Black Jack insists that he be isolated and will not operate until he is offered the key to the treasury vault. Midday through his progress, Black Jack discovers that the Prince was actually a princess all along. No sooner did Gor returned to the castle to seize the throne room that he saw Black Jack finishing his client. After the doctor reveals the truth that he kept his word but would not operate on the princess, Astro goes into battle with the sorcerer's monsters for one final conflict. Rock, who had disguised himself as Black Jack, finally captures and unmask the villain, who turns out to be Osamu Tezuka messing up his own mythology. Black Jack, after a worthwhile operation intent on reviving Sapphire, with his acknowledgement, lets her expose the truth of her secret life to her kingdom.

This episode has an Easter egg referencing the original Gundam. It can be seen as Uran walks past a playground on her way to class.

One evening, Astro is watching a story on TV about a boy who finds a bottle that contains a genie, who is released and promptly threatens to eat the boy. The boy instead asks to see if the genie can drink all the water in the sea; the genie grants his wish and drinks so much water that he explodes. As the story ends, a large meteor falls into a mountain valley some distance away. Dr. Elefun, Astro, and a team of scientists head off to investigate the crash. At the impact site, Astro uncovers a large metallic meteor-like object that turns out to be a mass of metal parts. Astro constructs the parts, and finds that they form a giant robot. A message capsule hidden in the mass calls the robot "Garon", which came from an alien planet and apparently has terraforming abilities. That night, a thunderstorm erupts, and Garon is brought to life by a stray bolt of lightning, frightening the scientists. Astro subdues Garon before he can cause damage, trapping him back in the impact site and buried in molten lava. However, one of the scientists, Dr. Adams, later uncovers Garon and secretly smuggles him to a remote island in the South Pacific. There, he requests Garon terraform the island to resemble the planet of his origin. As Garon proceeds to terraform the island, he also alters the atmosphere around the island to that of his planet. The scientists discover that his atmosphere has almost no oxygen content, but all perish before they can escape. The tradewinds begin carrying the poisonous atmosphere across the South Pacific, killing all life in its way. Astro is sent by Elefun to investigate, and he encounters Garon, still busily terraforming the island. Realizing that he can't win by brute force alone, he tricks Garon into also altering the gravity of the island to match that of his planet for at least one minute. Garon falls for his trick, and after altering the gravity of the island, gets shot back out into outer space, creating a vacuum around the island that pulls all of the poisonous gas along with him.

Alien invaders arrive in the Sol system and begin destroying space stations orbiting several of the planets. The nations of the world believe the attacks are those of Atlas, and unite to form a World Defense Force to stop Atlas. Captain Keeley, one of the squad leaders, is tasked to destroy Atlas, which he desires as revenge for the death of his brother, a scientist on one of the destroyed stations. Astro, however, wishes to reason with Atlas, but Keeley refuses and takes his squadron out to battle. Atlas arrives to battle Keeley's squadron, and when Astro confronts him about the attacks, Atlas claims he never attacked the stations; he had come because he had heard the humans were seeking him out. He instead decides to battle Astro instead, but Livian, who was watching their encounter, begs Astro not to fight Atlas, as the two are actually brothers; Atlas and Astro were born of the same template. Astro is shocked, and Atlas goads him into joining him, knowing the truth, but Astro can't bring himself to do so. Astro has a flashback of all of their previous encounters, and he begs Atlas to make the right choice. Keeley finds Astro, and reveals his key weapon: a laser that can damage Atlas's Omega Factor. Astro rushes to find Atlas to warn him about Keeley, but Atlas refuses to run; Keeley finds Atlas and shoots him with the laser, despite Astro's begging him not to. The invaders reveal themselves, and destroy most of Keeley's squadron. Back on Earth, Dr. Elefun studies the footage of the invaders, deducing that Atlas was telling the truth. Astro tells him that he and Atlas are brothers; Dr. Elefun recalls the theft of Astro's plans and realizes Astro is correct. Meanwhile, the WDF calls an emergency meeting to strategize a plan on stopping the invaders, who are heading straight for Earth. Keeley's squadron rush back to Earth, and Astro rushes to the rescue of many civilians until he collapses from energy exhaustion. He is found and brought to an emergency shelter with Elefun. Keeley contacts him and tells him that an invader squadron is coming from Saturn, and he confesses he was wrong about Atlas. Astro swears that he will protect all those that he knows and loves, and rushes to find Atlas to reason with him again. He gets ambushed by invaders, but Atlas finds him. Astro begs Atlas to help the humans fight the invaders, but Atlas stubbornly refuses, claiming he hopes all of the humans die. Astro rebuffs him by saying that not all humans are bad, and that many are good and kind, and see past Astro being a robot. Livian reasons with Atlas, saying that Astro fights out of love and not out of hatred, but Atlas thinks he is foolish. He tells Astro to tell the humans "Perish!", but Livian shows Atlas the battle between Keeley's squadron and the invaders. Keeley sacrifices himself to destroy several invaders, and Atlas joins the fray, destroying many more invaders. They find the invader's base, and Atlas warns Astro not to join, and tells him that they are truly brothers after all. Livian stays with Atlas, out of love, and the two give their lives to pull the entire base and the invader squadron out into deep space. Astro is heartbroken by his brother's sacrifice.

A strange snow begins to fall. The snow drains energy from everything it touches. Astro battles a leopard, which is controlled by a strange doctor, who wants control of all the energy in the city.

Astro, Dr. Elefun and some modern-day vikings search for the lost tomb of Odin, but don't quite find what they are expecting.

In a prologue, Astro Boy's creator Osamu Tezuka reveals a little secret about the robot boy: That his legs are actually those of a robot girl. The backstory behind this fact, the plot of this episode, is that Astro Boy is tasked to retrieve one of his own blueprint templates from a military fortress of the Grota Republic. He meets and bonds with Nuka (Nikki in the American dub), a sentient robot girl built from his very template, which unfortunately incorporates a neutron bomb, and in order to stop the bomb, the two robot children have to make a costly sacrifice: she must be completely dismantled in order to stop the bomb. Astro, having fallen in love with Nikki, stays with her till the very end. All that is left of her are her legs, which Astro takes to Dr. Elefun and asks him to switch his legs with hers, so that she could be a part of him forever. Elefun fulfills his request, and Astro happily takes off on more adventures.