Young Samurai Jack hears an account of one of his foreshadowers going to the threesome of Magical Monks to get a mystical sword to overthrow the shape-shifting wizard/immortal, Aku. The sword banishes Aku to a Wasteland he had created. Aku unexpectedly shows up, free from his banishment, and wrecks the city despite the efforts of the town's warriors. Young Jack is rescued by his mother, and watches as his hometown is destroyed.
Following this is a set of events. Jack learns astronomy on a Japanese fishing ship, horse riding in Arabia, stick fighting in Africa, reading and writing in Egypt, wrestling in Greece, archery in England, sailing from Scandinavian Vikings, axe throwing in Russia, spear throwing from Chinese nomads, and unarmed fighting and Chinese weaponry from Shaolin Monks.
Jack then finds his mother who gives him the sword. He releases his empire from slavery, then goes off to defeat Aku. After a long and colorful battle with Aku, Samurai Jack is flung into the far future, where he must quest to undo the future that is Aku.
Jack befriends some talking archeologist dogs and learns of his location: In the future shaped by years of Aku's evil reign. He vows to help the dogs gain their freedom from a life of enslaved jewel mining.
Aku learns of Jack's arrival in the future, and of the help he is giving the dogs. He sends a huge army of insect drones to destroy Jack and the dogs alike. Jack has been busy preparing many traps for them however, and when they arrive the battle begins in earnest.
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, there is more to the situation than meets the eye.
Samurai Jack befriends a future community 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.
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 it's 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?
Samurai Jack hears of a mysterious island which possesses a well that can grant any wish. He arrives at the island and discovers the well is not alone.
Aku places a bounty on Jack's head, but is disappointed by the failure of some inept hunters, so he creates an evil spirit-clone version of Jack to finish our hero off for good.
Jack hears tales about a race of amphibians living in an underwater city who have a time machine. He searches them out, and they agree to let him use the machine, but the creatures have not been entirely truthful. In fact they betray Jack to Aku in return for his promise to resurrect their sunken city. When Aku betrays them they first turn all their weapons against Aku, but that proves ineffective. They rescue Jack who uses his sword to drive Aku off - in return, all he asks is that they give him a large supply of fresh raw fish.
Called on by a mysterious voice, Jack overcomes many obstacles and booby traps to find who is calling him. Deep in the earth he finds it is a creature made from rock and lava, who immediately challenges Jack to a fight, but why did it call for Jack?
Jack starts to cross a very long and very narrow bridge. After a while, he meets a very large Scotsman crossing in the opposite direction. It being a very narrow bridge, neither is willing to back up to let the other pass. The resulting battle ends when they become handcuffed together by a pack of bounty hunters. The two must coordinate their efforts to escape through a swamp and they make it to a village where the hunters engage in some heavy firepower. Jack and the Scotsman free themselves and together take down the hunters. Of course, at the end it looks like another fight is burgeoning as they discuss which one will have the honor of buying the other a drink...
Jack joins a group of gangsters who work for Aku. He also agrees to help steal the heavily protected crystal that can give Aku power over the whole planet. Fortunately Jack has not become a traitor, but has his own plans of how to hand over the swag.
The tales of Jack's adventures have spread far and wide, and children are having fun acting out the stories. Aku, watching as the child playing him is chased around by Jack and major and minor characters from other episodes, becomes enraged and decides to spread a few stories of his own. However, it becomes apparent that he has no idea how to deal with the curious and questioning minds of youth as he calls all the children into a giant room and tells them ridiculously distorted fairy tales featuring first himself as the hero and then Jack as the villain.