Part I: The Beginning – Aku, an evil shape-shifting demon, devastates a boy Japanese prince's land and abducts his father, the Emperor. The prince’s mother sends him into exile, where he begins training around the world under various teachers. Returning to Japan as a young man, the prince receives a mystical katana and samurai's robes from his mother, then frees his father and people from Aku's minions. Despite the Emperor’s warnings, the prince advances on Aku’s tower. He defeats Aku in battle, but before he can strike the killing blow, Aku casts a spell to send him into the future.
Part II: The Samurai Called Jack – The samurai is plunged into a dystopian future world ruled by Aku, adopting the name "Jack" after hearing some urban aliens repeatedly call him this name. After getting in a fight at a nightclub, he is hired by a group of canine archaeologists to protect them from Aku's forces.
Part III: The First Fight – Armed with various weapons and traps, Jack single-handledly defeats a large army of Aku's "beetle-bots" and frees the dog archaeologists from being forced to mine crystals for Aku. He subsequently vows to fight the demon's oppression until he can return to the past.

Jack fights to free a species of enormous, hairy beasts called Woolies from a tyrannical alien race called Chritchellites, which has enslaved them and stripped them of their culture. In return, the leader of the Woolies bestows his wisdom upon Jack and offers him guidance to find a way back to the past.

After accidentally exposing a colony of scientists seeking to escape Earth, Jack trains as an astronaut to protect them from Aku's space-guarding insect robots. Jack has a chance to use their rocket ship's escape pod once the ship reaches light speed to travel back to his home time. However, while the ship prepares to jump to light speed, he decides to avoid the risk of the ship's destruction by defending it from a giant laser gun made of multiple wasp robots.

A talented warrior named Ikra joins Jack as he seeks a magical jewel that could send him back to his own time and can only be used by the pure of heart. Once they reach the gem, it scans them to see whether they are pure of heart and judges that Ikra is not, then spawns a monster that Ikra fights. After defeating the monster, she destroys the gem, revealing "herself" as Aku and derailing Jack's quest.

Jack learns of a powerful wishing well that could return him to the past but is guarded by three blind, deadly archers who protect it. He then recalls practicing martial arts in China with a blindfold to train his other senses besides sight and uses this method to dodge the archers' arrows and free them from having their vision and minds taken from them by the well. The archers tell Jack that the well binds those who make wishes upon it to do its bidding, so Jack destroys the evil spirit within.

Angered by the failure of his bounty hunters and mercenaries to defeat Jack, Aku uses the samurai's inner negative emotions to create a mirror image whose sole purpose is to destroy him. As Jack is frustrated by the sheer amount of enemies he has fought, he has difficulty defeating "Mad Jack" until he calms himself on the inside and dubs Mad Jack an illusion, destroying his evil counterpart's physical form.

When Jack hears rumors of a time portal being found in the underwater city of Oceanus, he sets out to find the city and is welcomed by its three alien inhabitants: Ringo, Guinness, and Connery, all members of the Triceraquin race. However, he soon discovers that the "time machine" is really a trap planned by Aku, who promised the Triceraquins a chance for their sunken city to return to the ocean surface if they were to successfully capture Jack. Aku betrays the aliens and tries to destroy their city and drown Jack, but Jack defends the aliens and forces Aku to flee. As a reward for successfully resurfacing Oceanus, the Triceraquins give Jack a large supply of sushi for his continued travels.

Inside a volcano, Jack survives a series of traps and encounters a Viking king whom Aku has imprisoned in solid rock. He has learned how to manipulate rock to form a humanoid body and insists that Jack slay him in battle. Jack initially refuses but learns that, in the king's current state, Aku has wrecked his chances of entering Valhalla. He breaks the rock body and frees the Viking inside, who ages rapidly. Jack places his sword in his hands before he dies a frail old man. Two valkyries arrive and take the Viking's body to Valhalla, where he is last seen watching over Jack with his youthful appearance restored and surrounded by various Norse gods.

While crossing a seemingly endless bridge in a region that resembles the American South, Jack runs into the Scotsman: a robust, aggressive, stereotypical Scottish warrior who also wields an enchanted sword. Their argument turns into a day-long fight that ends with them both exhausted and without a clear victor. After realizing that Aku has placed bounties on both of them, they join forces to escape into the swamp below, fight an army of bounty hunters, and form a new friendship.

Jack teams up with a quintet of diminutive 1920s to 1940s-type gangsters to try to get close to Aku. They send him on a heist to steal the mystical Jewel of Neptune, which can control all the world’s water, guarded by three elemental spirits who have fought to defend the jewel from Aku for centuries. Jack steals the jewel and travels with the gangsters to Aku’s lair, where they give Aku the jewel before Jack surprise-attacks him. As Jack is about to kill Aku, the gangsters knock him unconscious and escape, telling Jack that Aku was about to use another trick. The gangsters then lie about giving up crime to convince Jack to let them keep the jewel before he leaves them.

Seeking to weaken Jack's popularity among his subjects, Aku gathers the children of the world in his palace and tells them a series of "fairy tales", all of which portray himself as a hero and/or Jack as a villain. The children are not easily convinced by these stories, as they call out Aku for his inaccurate and often contradictory portrayals of himself and Jack. Aku leaves in frustration and failure while the children make up their own story about Jack heroically killing him.

Jack almost enters a time portal, which Aku then steals by raising it out of Jack’s reach. Jack tries jumping to enter the portal but cannot due to his lack of jumping skills. On his continued travels, he helps a peaceful tribe of apelike creatures and their human leader defend themselves against the attacks of a larger rival tribe in return for lessons on how to "jump good", which involves jumping to gravity-defying heights. He is last seen surprising Aku with his new abilities when Aku tries to steal another time portal.

Three short stories are presented in chronological order:

Jack vs. the Worm - Jack confronts a two-headed riddling worm that could grant his wish to return home. Upon answering a challenging question about which head always lies and which always tells the truth, he allows himself to be consumed by the "truth-teller", only to learn that both heads are liars and are not magical as he finds himself in the bowels of the worm and surrounded by a group of disheveled old men who were tricked by the worm as well.
The Metal-Eaters - A family who claims their village was destroyed by Aku joins Jack for a campfire dinner. He quickly learns that they feed on metal as they try to eat his katana. As he fights them, he soon discovers they are all robots, who then eat each other.
Jack, the Gargoyle and the Fairy - Jack sets out to rescue a fairy, who can grant a single wish in her lifetime, from being trapped in a magic orb by a gargoyle so she can grant his wish to return home. When he reaches in the orb, he finds his hand stuck inside, so he quietly tries to steal an amulet with a similar orb from the sleeping gargoyle. Jack accidentally awakens the gargoyle by making too much noise trying to free the fairy using only the amulet. After he kills the gargoyle, the fairy tells him that only the gargoyle knew the magic words to release her from captivity, so Jack wishes them both free.

Jack is captured and taken to the "Dome of Doom", where he forced to fight as a gladiator against the Dome's champions. He finds his missing sword on a wall of other stolen weapons but has trouble getting past various champions to reach it. As no weapon is illegal in the competition, he uses a variety of weapons to defeat three champions one at a time, then retrieves his sword and uses it to best five champions at once. He finally forces the arena's surprised owner and announcer to release his slaves.

The Scotsman invites Jack to help him rescue his kidnapped wife from robotic Celtic demons. To prove himself worthy for the mission, Jack must first gain the trust of the Scotsman's rowdy clan, who cannot help due to an ancient tradition. After passing a test of masculinity by throwing a muscular clan member over a great distance, Jack ventures with the Scotsman into the Castle of Boon, where the demons plan to cook the Scotsman's wife into a stew at midnight. The demons' leader, the Master of the Hunt, corners them as they try to rescue her. After he unintentionally insults the wife by calling her fat, she furiously overpowers the Master and his armies. The wife thanks Jack and her husband for their heroism, but as they prepare to leave the castle, Jack mentions that the doorway might be too small for her, prompting her to angrily chase him out as the castle collapses and the Scotsman begs her not to hurt Jack.

While investigating the destruction of several scattered villages, Jack learns that Aku's new "ultra-bot" assassins are responsible. Unable to destroy them, he hides in the ruins of a village and encounters a mad scientist tricked by Aku into creating the robots. He gives Jack a mechanical arm that grants him the strength to defeat seven of the assassins. When the arm runs out of power, Jack calls upon the spirits of his ancestors to enhance his sword's strength and destroy the last robot. Aku's dark energy leaks out of the robots and tries slithering away, but Jack destroys it, causing Aku to remotely feel the pain.

After Jack saves a village of raccoon-like creatures from mechanical cat cossacks riding grasshopper-like aircraft, he wanders the wilderness for a time and stumbles upon his ruined home town, including his family's estate. Jack then recalls some of his childhood memories. He first remembers chasing a grasshopper through a reed field and meeting a girl his age at the same game, who tried to help him pursue the grasshopper before it flew away. The girl gave Jack his first kiss when he made her an origami grasshopper. Coming across an empty river, Jack recounts watching a ronin fight four enemies on a bridge, sparking his interest in swordsmanship. Finally, rediscovering his favorite toy ball causes Jack to remember how he retrieved it from bullies by scaring a flock of birds in their direction. A robot calling for help snaps Jack out of his reminiscing, and he leaves while memories of his parents look on in pride at the man their son has become.

After another time portal is destroyed by Aku's beetle drones, a distraught Jack encounters three monks who have been training all their lives to climb the icy Mountain of Fatoom in search of what could be a mysterious power atop the mountain. He joins them on their expedition and fights goat-like humanoids, a rock monster, and a yeti-like creature along the way. Exhausted from battle and without his travelling companions nearby, Jack declares reaching the mountaintop impossible, then experiences visions of the monks reminding him of his purpose and urging him not to give up on his quest. He finally reaches the mountaintop and, despite finding no magical power there, shouts into the distance that he still intends to return to the past and destroy Aku.

Jack discovers a Medieval Europe-style village plagued by a foul stench. He asks the local "scissorsmith" about the stench's origin, and although the scissorsmith refuses to offer information without a fee, his talking pet crow reveals the stench comes from a dragon living in a mountain dubbed "the Spire". Atop the Spire, Jack finds the dragon has severe indigestion that causes colossal flatulence, so he navigates the dragon's complicated digestive system to arrive in the larger intestine and encounters the source of the stench: a baby dragon spitting fire from a partially-hatched egg. Jack is launched out of the dragon's rear end with the baby in tow, which hatches and flies him to safety. Back in the village, the residents rejoice about the end of the stench, ignoring the baby dragon causing chaos by breathing fire.

Aku challenges the Imakandi, regarded as the greatest hunters in the universe, to capture the ultimate prey: Jack.

Aku sends his servant Demongo, a demon who captures and enslaves the souls of warriors to serve him, to destroy Jack.

Jack must chase a mysterious thief who stole his clothing while he was bathing, but things get complicated when his pursuit leads him into another world, whose denizens could gaze on his nudity.

While ascending a mountain, Jack encounters a hidden society of warriors who have fought a nearly 500-year war against an army of robots and offers to help them put an end to it.

When a gang of robot bikers destroy his sandals, Jack seeks revenge, but realizes that he can't do so without footwear, something he has difficulty choosing.

Jack is transformed into a chicken after bumping into a cranky wizard and winds up being captured by a greedy man who seeks to turn him into a prizefighter.

Jack infiltrates a rave party after witnessing the participants stage a riot in a nearby town. It turns out that the DJ is one of Aku's servants, and has been using his music to hypnotize the local children into becoming his master's slaves.

Jack boards a train to his next destination, only to be pursued by legendary bounty hunter Ezekiel Clench and his ex-wife Josephine.

Aku leads Jack into a cursed graveyard, where he is attacked by an army of undead warriors. Jack defeats them, but then discovers Aku's true plan: kill Jack with his own sword.

Aku summons the three immortal servants of Set to destroy Jack while he travels through Egypt. To destroy them, Jack must assemble a golden scarab using clues from his time as a young boy.

Recognized as a mighty warrior, Jack is guided to a mysterious portal capable of returning him to the past. However, he learns that only one man can use the portal: the man who defeats its unbeatable legendary Guardian. The Guardian defeats Jack but spares him, prophesying that Jack is not yet ready.

While continuing on his mission, Jack is followed by an overly friendly creature who accidentally thwarts his every move. To make matters worse, he's attacked by robotic bounty hunters.

Jack meets a swamp hermit who guides him to the three gems of Cronus which can take him home, but the hermit is Aku in disguise.

Jack encounters a haunted house in his travels and must free the family trapped inside from the evil spirit haunting them.

Jack is attacked by two monks, who he realizes are members of the order he once trained with. Their master informs Jack of an ancient temple that can send him home, but which is protected by an army of stone warriors.

Centuries ago, the demon Aku is accidentally released by Jack's father, who receives a magic sword from the gods. Eventually, he uses the same sword to imprison Aku beneath the earth.

This hour-long episode won the Primetime Emmy Award for Outstanding Animated Program.

Jack finds a booby-trapped labyrinth, in the center of which is a diamond which could send him back to his own time. But a mysterious stranger, who has also entered the maze, could put Jack's plans in jeopardy.

Aku sends the Shinobi, a deadly assassin, to kill Jack, who must use his own martial arts to survive.

Jack uses a stone giant to defeat Mondo-Bot to defend a city of robots.

Jack is goaded into a duel by an arrogant bully called Da Samurai (voiced by David Alan Grier), and is given the chance to demonstrate the true ways of the warrior.

When Aku catches a cold and spreads it to Jack, Jack is accidentally infected with Aku's evil. Jack desperately seeks out a cure before Aku's essence transforms him into the monstrosity himself.

Five of the world's greatest bounty hunters gather to compete for the chance to kill Jack. A sixth hunter, revealed to be the princess of a fallen kingdom, persuades the group to work together instead.

Part I – The Scotsman suddenly discovers Jack aboard a ship with his memory completely lost. Refusing to let Jack think he's an ordinary commoner, the Scotsman sets out to discover what caused the samurai to suffer his amnesia. On the way, he befriends a gang of pirates and staves off bounty hunters pursuing a now defenseless Jack, who has forgotten how to wield his sword.
Part II – The source of Jack's amnesia is discovered in three beautiful sirens, whose bewitching song can hypnotize the strongest warrior.

The prince and princess of an alien planet are imprisoned by Aku when they come to Earth seeking his assistance and only Jack can rescue them.

Seeking to end their struggle, Aku proposes a one-on-one duel between him and Jack, with neither combatant using their magic abilities. Jack agrees, but Aku's honesty is unclear.

As he experiences summer, autumn, winter, and spring, Jack must overcome the dangerous foes he encounters during each season.

X-49, a retired robot hitman, is blackmailed by Aku into coming out of retirement to hunt down Jack.

While training in Africa as a child, Jack must save his master and his people from a rival tribe serving Aku.

Jack rescues a baby from hungry ogres, but then trying to find the child's mother while caring for it and protecting it may be his greatest challenge. During the episode, Jack retells the story of Momotarō^{[citation needed]} to the baby.