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.
Jack is infected with a bit of Aku and the piece infects him with Aku, trying to take him over and drive him to evil.
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 crews against him but use 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.
A prince and princess flee invaders of their planet and go for help, but ended up stranded on Earth and captured by Aku's forces - only Jack can rescue them.
Tiring of the failure of his minions, Aku decides to engage Jack in one-on-one combat to settle matters between them once and for all.
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.