When the ancient evil Aku returns to terrorize Japan, the emperor's young son is send to distant lands to train in the ways of the warrior. Only then can he wield his fathers magical sword to stop Aku from taking over the world.
Aku has transported his mortal samurai enemy into the far future in which Aku rules all. Now the warrior has to find a way back while adjusting to his new surroundings. He also takes a new name: Jack.
Aku's destroyer beetle drones are closing in on Samurai Jack and the pack of archaeologist dogs. Therefore Jack decides to use anything and everything at hand to defend themselves.
While hunting for food, Jack helps the tiny Chritchellites recapture an escaped Woolie. But once they invite him back to their village for dinner, Jack begins to suspect an unbalance in the pecking order.
Samurai Jack hooks up with a group of scientists who are secretly building a rocket to escape from Aku's service. When they hear about Jack's predicament, the scientist come up with a way to send him back in time.
Jack aided by an equally skilled warrior woman, to whom has a dark secret, search for a crystal with magical properties.
Jack learns about a wishing well of King Osric on top of a tower protected by three unbeatable archers and vows to make his way past them.
Despite a reward of Two Googooplex on his head, no bounty hunter has been able to defeat Samurai Jack. Therefore Aku creates an evenly matched mirror image of Jack to battle him.
Samurai Jack ventures into the deep end of the ocean after hearing of a time portal can be found in Oceanis, the sunken underwater city of the Triceraquin.
Having made his way through a cave filled with booby-traps, Samurai Jack faces a giant lava monster that used to be a viking warrior in days long past.
Samurai Jack is crossing a seemingly endless rope bridge when he meets another wanted man coming from the other side: the Scotsman. After fighting each other to a stalemate, they are forced to team-up when bounty hunters arrive on the scene and shackle Jack and the Scotsman to each other.
Samurai Jack gets an offer to join a Thirties style gang of mobsters at the Blue Monkey club and decides to take them up on it so he can get close to Aku. The gang plans to steal something Aku has been unable to obtain: the legendary Neptune Jewel, guarded by Earth, Wind and Fire.
Samurai Jack has become a popular folk hero amongst little children, so Aku decides to spread his own kind of fairy tales that put Jack in a bad light.