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.

While taking a trip on a Old West-style train, Jack is stalked by a bounty hunter, Ezekial Clench. He manages to defeat him but unwittingly falls prey to Ezekial's ex-wife Josephine.

Aku resolves to do something about The Samurai once and for all and lures him into a cemetery. Then the wizard unleashes hordes of the undead and one of the creatures manages to possess Jack's sword and deliver it to Aku. Armed with the sword and his own shape-shifting powers, Aku runs Jack ragged and then captures him and tries tohug him with the sword...which Jack finally remembers can't be used by the evil to harm the innocent. With the sword incapable of harming him, Jack regains his weapon and drives Aku away.

In the past during his training days in Egypt as a boy, the Samurai wandered into a temple and saw part of an ancient prophecy concerning Set. In the modern day, as he travels toward Egypt, Aku unearths three ancient Minions and tasks them tohug Jack in return for freeing them. The three creatures, armed with mystic weapons, prove more than a match for Jack but he remembers the prophecy. Unraveling a series of riddles, Jack assembles the three pieces and summons an ancient god to destroy the creatures.

To get to a time passage, Jack must pass a lake which sucks down any who try to cross it without touching its bottom. The locals summon an ancient creature who can walk upon the bottom but tall enough to stay above the water. It puts in a good word for two other creatures: a crawling creature that helps Jack pass a mountain and a flying creature that flies him to the portal. Jack must face its Guardian, a mighty warrior with an unlimited arsenal of weapons and incredible strength who says the only one who may pass is the one destined to use it. Ultimately Jack is defeated and the Guardian sends Jack back, as a mysterious warrior (apparently an older bearded version of Jack) within the time passage apparently tells the Guardian that Jack can't use it . . . yet.

Whilst crossing a desert to seek the Crystal of Cagliostoro, Jack comes across a oasis. He unwittingly disturbs an overly friendly creature, who begins following Jack, messing up Jack's every move along his quest. After the creature eats the Crystal, Jack spurns the creature who even more upset to discover in the morning that Jack has abandoned him. Jack meanwhile runs into some mean bots that are more than a match for him. On hearing Jack's cry of pain and seeing him unconscious, the creature becomes enraged and transforms into its vicious form to defeat the robots. Jack wakes up and is left to wonder what happened to the robots.

Jack finds a swamp where a foul-tempered hermit answers his call. The wizard tells Jack of the titan Chronos and his powers over space and time, now locked within three pieces of armor set with gems.
Three trap-solving sequences follow - the helmet is hidden in a water trap, one gauntlet in a volcanic air trap, and the second gauntlet in a lens-dome. Jack manages to defeat all three traps and Aku uses the armor/gems to summon a time-space-monster tohug Jack.
Jack realized that it had been a trap all along and took one of the gems, causing the creature to fall apart, and then goes after Aku. Jack manages to slice and dice his way through anything Aku throws at him with surprising ease - Aku flees as a triumphant Jack speaking of how the future/past holds his victory.

Jack travels through a beautifully animated swampland, when he comes across a small shadow crying in the distance. After approaching the being, it drops a small toy doll and Jack follows it back to a small house in hopes of giving the item back to the creature. Jack travels through the house, taking on the memory of a family, ravaged by some creature, with each specific items unlocking these horror filled dreams. Jack finally uncovers the owner of the doll, a little girl, and also discovers that all the windows or doors have disappeared. Later Jack awakens to see the little girl gone, only to find in a beautiful room with the family Jack sees in his visions. Although the family pretends nothing is amiss, eventually each lets out strange light from their mouths which forms into a large shadowy dragon beast that devours Jack, allowing him to see the family trapped inside.

Jack meets two Shaolin monks and after a brief fight he convinces them of his credentials and they take him to see their Grand Master at their hidden temple. The Master was at the temple when Jack studied there and remembers him. The Master directs Jack to a gateway that opens at noon and he and the two monks travel to the tower it is atop. Moving up the tower's catwalks they must fight a seemingly endless horde of stone statues. Jack gets to the portal but turns back to help the two monks rather then make his escape. The three of them escape the statues by destroying the tower and his time portal.

The gods Odin, Ra, and Rama battle a great dark evil. One shard escapes and falls to primitive Earth, creating a vast black forest. Down through the millennia it spreads andhugs until the period of feudal Japan. An emperor and his army set out to fight the evil with the aid of a mystical elixir. His army is wiped out but the emperor fires an arrow covered with the elixir into the heart of the darkness, but only sets it free and gives it voice and face: Aku. Aku imprisons the Emperor and wipes out his lands.

The gods send the Emperor a mystical horse to free him and deliver him to a castle in the sky. The three gods give him powers and forge a mystic sword for him to wield. The Emperor goes forth to fight Aku. Aku is vulnerable to the sword but his shape shifting abilities prove the Emperor's equal, particularly when Aku takes on the form of an entire army. But the Emperor manages to prove seemingly triumphant and the Emperor's wife greets him with his newborn son. The Emperor resolves that in case Aku returns, he must formulate a plan.

Jack is directed to a passingtrap-filled labyrinth which holds a diamond that can restore him to his time. Unfortunately a master Thief also enters the labyrinth going for the item. The two of them prove equally adept in their own styles of bypassing the same traps through technology and training. The two men are forced to alternately join forces to defeat the guardian statue-robots and double-cross each other to make sure they end up with the gem. Jack helps the Thief escape who in return leaves him trapped - overwhelmed, Jack is on the verge of defeat when the Thief returns to pull him out. The two seem to come to terms...just as the diamond shatters and the Thief apparently disappears.