Aku, an evil shape-shifting demon, devastates a young prince's land, and his parents send him into exile. After years of intensive training, the prince receives a mystical sword and samurai's robes, and frees his people from Aku's minions. He then defeats Aku in battle, but before striking the final blow the latter casts a spell to send him into the future.
The samurai is plunged into a dystopian world ruled by Aku, adopting the name "Jack". After getting in a fight at a nightclub, he is hired by a group of canine miners to protect them from Aku's forces.
Armed with various weapons and traps, Jack single-handledly defeats Aku's "beetle-bots". He subsequently vows to fight the demon's oppression until he can return to the past.
Jack comes in contact with a tribe of creatures who utilize their technology to subdue a group of supposedly savage beasts called "Woolies". Little does Jack know, there is more to the situation than meets the eye.
Samurai Jack befriends a colony of scientists building a spaceship to escape Aku's tyrannic rule. Jack agrees to assist in their escape by fighting off the blockade orbiting the planet in return for a trip through time back home.
A talented warrior named Ikra joins Jack as he seeks a magical jewel that could send him back to his own time. However, Ikra's true motives threaten to derail his quest.
Jack learns of a powerful wishing well that can return him to the past, but must find a way past the three deadly archers who protect it.
Angered by the failure of his bounty hunters and mercenaries to defeat Jack, Aku uses the samurai's inner darkness to create a mirror image whose sole purpose is to destroy him.
When Jack hears tales of a race of amphibians living in the underwater city of Oceanus in possession of a time machine, Jack sets out to the city and is welcomed by its Triceraquins, but is unprepared for a terrible surprise.
Called on by a mysterious voice coming from a nearby volcano, Jack overcomes many obstacles and booby traps to find a Viking king transformed into a giant rock figure by Aku, who insists that Jack slay him in battle so that he may reach Valhalla.
While crossing a seemingly endless bridge, Jack runs into the Scotsman: a robust, if impulsive, stereotypical Scottish warrior who also wields an enchanted sword. Their argument turns into a fight that causes them to both fall off the bridge. After realizing that Aku has placed bounties on both of them, however, they join forces to escape and form a new friendship.
Jack teams up with some gangsters to try to get close to Aku. The only way to do it is to get a mystical jewel guarded by three elementals.
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 Jack as the villain.