Jack searches for the the magical jewel the Woolies told him would be able to send him back in time. Locating the last survivor of the race who can reveal its location, Jack learns of how to find the jewel, and meets up with a woman questing for the same jewel. They journey through the desert together, but will they be able to share the jewel if they find it?
Jack tries to save a peaceful tribe that move constantly due to an opposing food-stealing tribe of monkey/lions: Jack meets up with the Monkey Boy who can "jump good" almost to the point of flying. Jack is taken to his village and agrees to teach a group of furry creatures to fend for themselves in return for "jumping good" lessons. Jack teaches the creatures to use bamboo to fight and together they set up an array of traps for the monkey/lions. In return Jack has a challenging time trying to "jump good", a process involving climbing hills and vines ... with boulders attached to his body.
Jack is kidnapped and placed in a chain gang of warriors chosen to battle in the Dome of Doom, against the Smackback Ultimate Champions. Even without his sword, Jack defeats Gordo and the Aqualizer, and then must defeat the massive but ticklish Sumoto with the aid of his top knot. In desperation the Ringleader sends his remaining gladiators after Jack, who defeats them handily and forces the Ringleader to release the gladiator-slaves.
After defeating a band of robotic cat-demons Jack travels the land and finds himself in the area where he grew up. As he tours the ruins he has flashbacks to a day spent pursuing a locust in the company of a young girl, witnessing a wandering warrior defeat four men on a bridge, having his parents greet him, and tricking three bullies.
After Aku's beetle drones destroy yet another gateway to the past, only moments before he's is able to reach it, Jack is overcome with frustration and is about ready to give up the quest. Then, by chance, he meets three monks about to climb the Mountain of Fatoom. Where, legend has it, truth can be found at the top.
Jack discovers a village of panicky medieval serfs, overwhelmed and unable to earn their livelihood because of a horrible stench coming from a nearby mountain. After getting some more information from a demented scissorsmith, Jack heads to "The Spire" to deal with the source of this stink: a fire-breathing dragon who needs Jack's help in dealing with some serious indigestion!
On an alien planet, Aku contacts four Emikandi hunters and offers them the chance to hunt Jack. They capture Jack with incredible ease but Jack just as easily frees himself after he hears they're working for Aku and the real hunt begins! After an extended chase the two sides battle atop a skyscraper and Jack falls to his death...but the hunters rescue him out of respect for their greatest prey. Then the Emikandi refuse to give him to Aku out of respect for Jack's skill and depart.
Jack bumps into an old wizard who transforms him into a chicken - a rather goofy-looking master of the martial arts that nobody can understand. He gets captured and taken to a animal fight where he must defeat a robot beetle and snake. Jack wins but must then fight a spider-like creature, a giant worm, and the ratlike mechanical "Finisher". Jack's series of wins make his new owner a wealthy man but when he goes out to buy some decent clothing he bumps into the same wizard who hits them both with a spell - causing Jack to become human and the owner to become a chicken. Jack departs with a new found appreciation for the virtues of not eating chicken.
In his travels Jack comes to a tavern and a crying tavern owner. Then shadowy figures attack but Jack discovers they are teenagers, the "Children of Aku", under a magical musical spell. Knocking one out and following them in disguise, jack finds their rave and a sinister DJ playing the music. The DJ spots Jack and a fight ensues. Jack takes the fight directly to the DJ who is his near-equal. When Jack gets the upper hand the DJ dons a speaker-battlesuit but Jack regains his lost sword at the last minute and triumphs, freeing the children.
Aku sends forth the robotic ninja Shinobi, Warrior of the Dark, to kill the Samurai. Jack responds to the cries of a young boy from a village beset by robot lobsters. Jack defeats them all while Shinobi watches - then the ninja takes the boy to a nearby ruined tower where he strikes from the darkness at Jack as he follows. Jack knows of the ninja's technique and reveals that he is trained to blend with the light just as Shinobi can blend with the dark. The warriors of light and dark fight from shadow to light and back again - with the sun going down, Jack quickly runs out of concealment and in a last desperate measure reflects the waning light onto Shinobi and destroys him with a well-tossed sword.
Jack enters the abandoned city of Andromeda and finds himself under attack by a monstrous giant robot, the Mondo-Bot. Jack is initially defeated and rescued by local robots who believe he is the Chosen One. The city is built on a magical city of giants and Jack goes underwater to seek them out and finds a giant samurai robot which pulls Jack into it. Jack's bot is resistant to everything the Mondo-Bot shoots at it so the two engage in an enormous close combat battle and Jack proves triumphant.
While traveling through the rain, Jack takes refuge in an inn and meets Da Samurai, a hip-hop singer/fighter. His performance is interrupted by a new version of Aku's bounty hunters. Jack defeats them handily, much to Da Samurai's amazement. Da Samurai challenges him to battle and Jack eventually agrees. Jack requires him to first fight with sticks and Jack is clearly the superior warrior. Their fight is interrupted by the arrival of many more of Aku's hunters. Da Samurai is captured and Jack defeats the 100+ robots...but they assemble into one gigantic multi-headed robot. Da Samurai saves Jack by taking an energy blast, giving Jack time to defeat the robot and acknowledge Da Samurai has taken the first step on the path of a true warrior.
Bounty hunters come together and vie among themselves to determine who will go first. Each hunter outlines his plan while another, armored hunter points out the flaws in each plan. The armored hunter is a woman, Princess Mira and she proposes they fight together, but she claim the bounty so that Aku will free her people.. The bounty hunters prepare their trap, digging pits to ambush Jack. But Jack defeats them all in the span of a second and even the princess yields before his superior ability.
While traveling the Scotsman finds Samurai Jack working as a waiter named Brent Worthington. The Scotsman rescues the amnesiac Jack from bounty hunters and realizes that Jack was injured by the tango beast. He follows the trail from the tango beast to a bar of bounty hunters to a sea captain to a chart that directs them to The Great Unknown. The Scotsman hires a ship to take them there.
The ship sails into the Great Unknown and encounters sirens who hypnotize everyone except the Scotsman who is conveniently immune thanks to his musical taste for Scottish music and his wife's singing. The entranced crew bring the ship to ground and give the sirens all their treasure as the Scotsman confronts the Sirens. They send the crew against him but he uses his bagpipes to snap them out of it. While the Sirens attack the defenseless Scotsman, Jack grabs his sword and kills the beasts. When the other ships leave without them and they have to have a series of contests to determine who will row the boat. Jack wins them all, including an epic thumb-wrestling battle.
Four separate stories following Jack through the four seasons: Summer, Fall, Winter and Spring. In Summer, Jack is traveling through the desert and is set upon by strange creatures formed of sandstorms. In Fall, a creepy little scientist attempts to make a poison to kill Jack. In Winter, a warrior race forge a mighty sword with which to slay Jack. In Spring, Jack finds rest in a mysterious garden paradise.
The first three-fourths of the story is a monologue: a Terminator-like killer robot with human emotions tells us the story of his life. He formerly worked for Aku, but stopped because of his emotions and because he felt in love with a little dog. But Aku kidnapped his dog and forces him to fight against Jack if he wants to see it again. He is tracking Jack and he is finally destroyed by the samurai His last words are for his puppy and Jack looks sadly at him. Then there is a close-up of his car and the last image of the episode is a photo of the dog.
This episode takes place during Jack's childhood. After Aku's first attack, Jack is brought to a tribe in Africa where he is admitted into the adult community after a small ritual and the chief of the village teaches him the art of fighting with a stick. But an enemy tribe attacks the village in order to get a reward promised by Aku for Jack's capture and everyone is captured except for Jack. So he follows them, mastering the captors' weapon, using qualities of the animals he has observed to do so. After a difficult series of fights, Jack releases all the prisoners and with their help, the enemy tribe is defeated. At the end, Jack leaves the tribe because he is now considered to have learned all he can from them.
While peacefully enjoying a snack of peaches, Jack hears a baby cry and races to find out what's the matter. He rescues Baby from a crew of hungry (baby-eating) monsters. The two then set off to find the baby's mother. Jack makes a great temporary parent, finding food, shelter, dealing with diapers. He tells Baby a bedtime story of Momotaro (Peach-boy, an archetypal Japanese folk-tale). When sick, Baby wants peaches; when they return to the peach orchard, the monsters find them again. After the final defeat of the monsters, Baby's mother is found. When she notices a surprising change in her child, Jack explains the baby has achieved sakai, the spirit of the samurai.
It's been 50 years since we last saw Samurai Jack, and time has not been kind to him. Aku has destroyed every time portal, and Jack has stopped aging, a side effect of time travel. It seems he is cursed to roam the land for all eternity. His past haunts him as does a cult of assassins dedicated to killing him for Aku's glory.