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- The Beginning: The ancient shapeshifting demon Aku is freed from his imprisonment and razes the lands of Feudal Japan. The warrior who sealed him all those years ago sends his young son sent off to be trained in faraway lands. He returns a grown man and battles Aku with the magic sword that will slay the evil being.note
- The Samurai Called Jack: In his battle against Aku, the nameless samurai is flung untold millennia into the future and finds himself in a strange dystopia ruled by Aku and populated by aliens, robots, and all manner of beings. There, he earns the appellation Jack from a gang of jive-talkers and encounters a group of talking archaeologist dogs who wish to be freed of Aku's slavery.note
- The First Fight: Having been informed of the samurai's reappearance, Aku sends out a massive army of insectoid robots to defeat Jack. Now, Jack will have to work with his newfound allies and use every skill he knows to earn his first victory against the forces of evil.note
- Jack, the Woolies, and the Chritchellites: Jack's travels in search for a way to return to his own time and undo Aku's dictatorship brings him in contact with the diminutive Chritchellites who ride large beasts called Woolies. The Chritchellites are cruel towards their beasts of burden, but Jack soon finds that the Woolies are not really simple animals.
- Jack in Space: Jack encounters a group of astronauts who seek to escape Aku by building a rocket ship. They also agree to help Jack return to his time via a lightspeed wormhole. However, Aku's insectoid machine soldiers and orbital defenses means they have little room for mistakes.
- Jack and the Warrior Woman: Jack encounters a skilled and beautiful warrior woman while traversing a desert. Both have been told about the existence of a jewel in the sands that will grant wishes to the pure of heart. However, the mystery about the warrior woman has an answer that Jack would be much happier having left unanswered.
- Jack and the Three Blind Archers: Jack is informed about a wishing well located in a tower on an island by a Viking warrior who saw it firsthand. However, as the Viking warns him, the well tower is guarded by a trio of sightless master archers. If he is to reach the tower, Jack will have to master fighting against and as a blind warrior.
- Jack vs. Mad Jack: As Jack staves off the seemingly endless stream of bounty hunters sent by Aku to destroy him at every turn, Aku begins to realize that he must defeat Jack with a clone of the samurai. So, Aku creates Mad Jack, a replica of the warrior's increasing fury against Aku's minions. Now, Jack must literally face his inner demon.
- Jack Under the Sea: Jack is informed by a fisherman about the underwater city of Oceanus, which has a time machine, so Jack dives into the darks depths of the ocean, where he encounters the Triceraquins, the amphibious denizens of Oceanus whose city was sunken by Aku. There, the Triceraquins agree to let Jack use the time machine, but their real plans are far more sinister.
- Jack and the Lava Monster: Jack finds a subterranean volcanic labyrinth filled with traps and echoing the voice of somebody beckoning him in. Following it takes him to a monster of lava who demands that Jack must fell him in battle or be slain himself, as the monster is a Viking warrior cursed by Aku to never ascend to Valhalla. Can Jack deliver the Viking an honourable death?
- Jack and the Scotsman: While travelling an impossibly long and narrow suspension bridge, Jack meets the Scotsman, a warrior with a bounty on his head as big as his. The two don't get off to a good start, but when bounty hunters manage to bound the two, the greatest warriors in the land will have to put aside their differences to be freed.
- Jack and the Gangsters: In a crime-ridden city, Jack befriends a group of midget gangsters who are planning to steal the Neptune Jewel, a gem capable of controlling water and guarded by elemental spirits, and give it to Aku as a gift. The gangsters are hoping to rely on Jack's skills in combat to defeat the elementals for them, but Jack wants to use the opportunity to fight Aku again.
- Aku's Fairy Tales: As word of Jack's amazing feats spreads across the lands and inspires children everywhere, Aku decides to take action. Bringing every child in the capital of his realm to a stadium, he tries to wow them with Fractured Fairy Tales featuring Jack as the villain. Hilarity Ensues.
- Jack Learns to Jump Good: After Aku wrests a time portal away from Jack's reach, Jack encounters a wild man living amongst a tribe of monkeys able to leap to stupendous heights like they were flying. They agree to teach Jack their ways in jumping and in return, Jack teaches them how to fight against a tribe of apes that constantly raid them.
- Jack Tales: In this trio of unrelated vignettes, Jack encounters a giant two-headed worm that supposedly grants wishes, battles a strange family that desires to eat his sword, and gets his hand trapped in a magic orb carrying a wish-granting fairy and guarded by a gargoyle who owns the key to escape.
- Jack and the Smackback: Jack is captured by slavedrivers who take him to the Dome of Doom, a massive gladiatorial arena where hapless captives are pitted against the deadliest fighters in the world. Separated from his magic sword, Jack must not only survive the gladiators with new tactics, but also escape the arena and free the other slaves.
- Jack and the Scotsman II: The Scotsman returns to ask Jack for assistance. His wife has been captured by a demon to be eaten in a stew, and the Scotsman doesn't have the strength to rescue her by himself. So, the two mighty warriors team up once more, briefly stopping at the Scotsman's clan castle where Jack must pass a test of worthiness before they head out.
- Jack and the Ultra-Robots: Jack follows a trail of ravaged villages and slaughtered innocents in search of the monsters behind the carnage. The culprits eventually reveal themselves to be a group of robots far advanced than any others and powered not by electricity, but by Aku's evil. The killer machines prove to be far too powerful, but their creator Extor is willing to help Jack.
- Jack Remembers the Past: Jack comes across the ruins of a settlement. Further inspection reveals that it isn't any old town, but the place where Jack was born and spent his early childhood in. Jack takes the time to wander about the ruins and the memories of happier times come flooding back to him.
- Jack and the Monks: Jack encounters a trio of mysterious monks who seek to climb a sky-high mountain, which according to legend, has a great secret of wisdom at its very peak. The thing is, nobody has ever climbed it successfully before. So Jack becomes determined to become the first, but as he scales the mountain, the challenges begin to wear down on him.
- Jack and the Farting Dragon: Jack comes across a town plagued by a terrible stench, which he is told comes down from a mountain spire home to a dragon. Upon reaching his destination, Jack finds the culprit is the dragon, who has a serious flatulence problem and begs Jack to help him, so Jack must travel through the dragon's body in search of the source.
- Jack and the Hunters: Aku travels to a distant world where he hires a band of five tribal hunters from a leonine race called the Imakandi to hunt Jack. The Imakandi, who live for the thrill of the hunt, agree and are transported to Earth to hunt their greatest game. Now Jack must outrun and outwit the greatest hunters in the universe.
- Jack vs. Demongo, the Soul Collector: Aku sends in his latest and greatest minion after Jack - Demongo, a fiend who collects the souls of warriors. Demongo is keen on adding Jack to his collection and the samurai finds that Demongo can summon the souls of those he captures to battle endlessly for him. How will Jack defeat Demongo and his constant stream of warriors?
- Jack is Naked: While bathing in a natural pool, Jack's robes and sword are stolen by a white rabbit. Chasing the rabbit naked leads him into a strange underground realm strongly based on the works of Lewis Caroll, where the clothes he puts on as temporary substitutes get him into all kinds of shenanigans with the locals.
- Jack and the Spartans: In this homage to The 300 Spartans Jack comes across an army of 300 Spartan warriors who have been battling against legions of robot minotaurs created by a living factory past the mountains in an endless stalemate. With Jack on the scene, the Spartans gain knowledge of how to reach the factory and the king and Jack head off to put the war to an end.
- Jack's Sandals: While he is dipping his feet in a riverside one day, a gang of robot bikers destroy Jack's precious wooden sandals. Jack pursues the robots to a nearby city, where they are causing chaos for their amusement. However, Jack's lack of footwear means he can't fight without hurting his feet, so he tries to find a replacement.
- Chicken Jack: In the midst of a big city, Jack accidentally bumps into an ill-tempered wizard who transforms Jack into a chicken as punishment. Before Jack can catch up with the wizard, he is captured by a man who uses Jack as a fighting cock for his battle dome. Now, Jack is stuck fighting the countless robot beasts pitted against him.
- Jack and the Rave: Jack stays at an inn for the night, but finds that the inn's owner is extremely sad because his teenage daughter went to a rave and has been turned evil by the rave's music - which is from Aku himself. To save her and all the other teenagers there, Jack will have to infiltrate the rave and destroy the source of the corrupting music - a task far more difficult than it sounds.
- The Good, the Bad, and the Beautiful: Jack boards a train to his next destination, but unbeknownst to him, he is being followed by two bounty hunters - an ugly fellow with mechanical hands named Zeke and a Femme Fatale named Josephine. However, Zeke and Josephine are a divorced Outlaw Couple and now have to deal with both Jack and each other.
- Jack and the Zombies: Aku manages to lure Jack into a massive cemetery where he uses his dark magic to resurrect legions of zombies to destroy Jack. All throughout the night, Jack battles endless hordes of the restless dead that become more and more frightening until one manages to steal Jack's sword and give it to Aku. Now, Jack must face against his own weapon in the hands of his enemy.
- Jack in Egypt: In the ruins of Ancient Egypt, Aku opens the tomb of the Minions of Set - three ancient evils sealed long ago - and instructs them to destroy Jack. Now, in the desert night, the samurai finds himself hopelessly outclassed by the servants of the dark god, leaving him with no choice but to elude them and complete the ancient riddles that hold the key to their defeat.
- Jack and the Traveling Creatures: Jack seeks a time portal once more, but to get there he must pass a lake that drowns any who cannot touch its bottom while walking, as well as mountains. Fortunately for Jack, three great beasts will help him travel - a long-legged lake monster, a many-legged mountain creature, and a giant pterosaur. But, the greater challenge will be the portal's guardian.
- Jack and the Creature: Jack searches for the Crystal of Cagliostro, which will supposedly take him back through time. However, on the way, he encounters a strange creature that looks an awful lot like Totoro. Although the creature means no malice towards Jack, it causes much frustration for the samurai on his journey through its goofy antics.
- Jack and the Swamp Wizard: Jack encounters a legendary swamp hermit of great magical power. The diminutive sorcerer agrees to help Jack get back to the past, but to do so, Jack must find the Armour of Cronus - time-warping helmet and gauntlets once owned by the king of the Titans. Each piece of armour is guarded well, but the little old marsh mystic is really a disguised Aku with a scheme in mind.
- Jack and the Haunted House: While travelling a dark forest, Jack encounters a terrified little girl and follows her to an abandoned feudal Japanese castle. While trying to search for the girl and give her back the teddy bear she dropped, Jack is plagued by disturbing visions. Soon, it becomes apparent that an evil spirit haunts the castle and its after Jack and the girl.
- Jack, the Monks, and the Ancient Master's Son: Jack's travels bring him to the Shaolin temple he trained at during his youth. There, the son of his master, now an old man at one with the universe, tells him of a time portal on a mountain that only opens for a few minutes every midday. So, Jack and two other monks head out, but hordes of stone soldiers guard the mountain pathways.
- The Birth of Evil: Aku's origin story is finally unfolded as a vestigial piece of a nameless abomination of darkness defeated at the beginning of time by the combined forces of Vishnu, Ra, and Odin crashlands on Earth in the Mesozoic and spreads its evil from a fetid pit in a forest of spikes until the Feudal Era where Jack's father's attempt to destroy the evil gives it self-awareness.
- The Birth of Evil Part 2: The origin of Jack's sword is told as Jack's father is left helpless as Aku ravages his kingdom. But the three divine powers that defeated the mass of evil so long ago bring the emperor to a sacred mountaintop where they forge a sword out of his righteousness. With his newfound strength, Jack's father returns home to defeat Aku.
- Jack and the Labyrinth: Jack enters a labyrinth-pyramid which contains a magical diamond of great power in its center. However, he is not the only one having to overcome the pyramid's challenges though, as a superspy also seeks the diamond. Inevitably, the two meet each other and must fight for the diamond as well as escape the pyramid's guardians.
- Samurai vs. Ninja: Aku sends a ninja after Jack this time, and while Jack is battling giant mechanical lobsters attacking a seaside village, the ninja follows him in the shadows without notice. When the ninja kidnaps a boy to lure Jack to a tower filled with old beams under the setting sun, the hero finds that the best way to fight those who hide in the darkness is to hide in the light.
- Robo-Samurai vs. Mondo-Bot: Jack is attacked by a colossal machine in a ruined city. Outsized by his enemy, he is rescued by a group of robots who tell him that his attacker was Mondo-Bot, a gigantic automaton gone berserk. Believing him to be "the chosen one" they send Jack to the ruins of a giant's city where he merges with a humongous samurai robot to battle Mondo-Bot.
- Samurai vs. Samurai: One rainy day at a tavern, Jack meets a loudmouthed jerk who claims to be the greatest samurai in the world. He challenges Jack to a duel outside, where Jack and the phony battle with sticks of bamboo (under Jack's request). Jack intends to teach the fool a lesson in humility through the duel, but Aku's newest line of robot assassins interrupt the lesson.
- The Aku Infection: During a battle with a sick Aku, Jack catches a cold from him. But this is no ordinary illness, for it begins to spread through Jack's veins, turning him every bit as evil as his enemy. Desperate for help, he heads for a cave temple run by lizard-monks who guard a time portal. However, the only way to completely purge pure evil from the body will be Jack's inner strength.
- The Princess and the Bounty Hunters: In a snowy countryside, a gang of the world's most ruthless bounty hunters consisting of an aboriginal darter, a pair of Siamese cat-like twins, a gentleman knife fighter, and a large Russian man team up with a fierce warrior princess named Mira. Their goal - to capture Samurai Jack, of course.
- The Scotsman Saves Jack Part 1: While on board a ship, the Scotsman notices Jack dressed as a cabin boy. Speaking with the samurai, he finds that Jack is now a peace-loving simpleton named Brent Worthington and no longer has his sword with him. Determined to restore his friend's state of mind to normal and find his sword, the Scotsman heads out in search of clues to what had happened.
- The Scotsman Saves Jack Part 2: At a scummy port city, the Scotsman manages to convince some pirates to take him and the amnesiac Jack to the Great Unknown, a region of the ocean where boats mysteriously vanish and Jack lost his memory. There, a hauntingly beautiful song hypnotizes all except the Scotsman (who thinks its horrible) and lures them to the cave of the Sirens.
- Jack and the Flying Prince and Princess: On the faraway planet of Chrysalis, home of the butterfly-like Lepidopterans, the prince Aster and princess Rabina are sent to call back troops away from home when their planet's enemies attack. Unfortunately, a problem in their spaceship forces them to land on Earth where Aku enslaves them, but a sympathetic Jack is following them close behind.
- Jack vs. Aku: Fed up with the constant failures of is minions, Aku decides to take matters into his own hands. He heads off to Jack and demands Jack to battle him one on one at some ruins. Jack agrees under the condition that Aku must not use his powers and fight him only with the form of a man while Jack will not use his sword. Aku agrees, but at the duel, things are a little different.
- The Four Seasons of Death: In this collection of themed vignettes, Jack battles elusive desert phantoms in the summer, an evil scientist collects fallen leaves to concoct a deadly poison in fall, a tribe of mountain-dwelling orcs forge a powerful sword to use against intruders in winter, and a nature spirit attempts to get Jack to stay with her forever in spring.
- The Tale Of X9: In this Film Noir-style episode, a retired robot hitman named X9 tells the story about how he was built with emotions and befriended a dog named Lulu during his career. However, X9's peaceful retiree life with his dog is cut short when Aku kidnaps Lulu and tells him that he'll only get the dog back if he kills Samurai Jack.
- Young Jack in Africa: In this flashback episode, the young Jack trains in the art of combat on the African savannah under the guidance of a tribal chief, while also frolicking with the chief's son. However, when a wicked tribe is enticed by Aku to capture the tribe, it is up to Jack to save them with all that he has learned.
- Jack and the Baby: While collecting peaches in peach forest, Jack overhears the crying of a baby, which leads him to a gang of trolls planning to eat an infant. Jack manages to rescue the baby from their clutches, but now has to find the baby's parents. As he travels around, Jack cares for the baby and reminiscences on the story of Momotaro the Peach Boy.