After learning none of the Shen-Gong-Wu can stop Wuya, the Xiaolin Apprentices team up with Jack. They figure out the only way they can put an end to Wuya's reign is to travel back in time 1500 years, where Grandmaster Dashi first defeated her. Omi goes through Jack's time machine alone with only one Shen-Gong-Wu, leaving the rest with the other three to protect themselves. Omi's plan is to find Dashi and receive another puzzlebox to trap Wuya in.
With Omi still trapped in the past, the Dragons and Jack Spicer are captured by Wuya's evil forces. The final chapter is at hand, and Raimundo must come to gripes on where he belongs...
After KatnappÃ© releases Wuya from the puzzle box, the two form an unhealthy alliance. Jack builds another robot, but this time, it's a clone of himself, who is much quicker, smarter, and gets all the good jokes. Jack and his clone use the newest Shen-Gong-Wu, Shard of Lightning, to freeze time and quickly steal most of the Warriors' Shen-Gong-Wu. The Warriors must think of a plan to stop them, while Wuya starts to regret teaming up with KatnappÃ©.
After helping the Warriors acquire a new Shen-Gong-Wu, a Russian vendor named Vlad joins the Xiaolin Dragons-in-training. When Omi uses the new Shen-Gong-Wu, Crystal Glasses, he sees that he becomes evil in the future. Upon seeing this, he quickly leaves the Xiaolin Temple, deciding that he can no longer continue to be a Xiaolin Dragon-in-training.
Jack stupidly sells all his Shen-Gong-Wu, except for the Monkey Staff, in order to buy robot parts so he can build a robot servant. He sells them to Pandabubba, the crime boss that works in Hong Kong's underworld. Pandabubba sends his henchmen all over Hong Kong, equipped with the Shen-Gong-Wu, to loot. The Xiaolin Warriors must figure out a way to stop them, but their faith lacks in Raimundo, as he still isn't a Xiaolin Apprentice.
Jack and Wuya have a new minion - Cyclops, a one-eyed monster that's short on brains but long on strength and size, who is seemingly unstoppable. In order to combat this new threat, Omi simultaneously uses the Changing Chopsticks and Reversing Mirror to super-size himself. But size isn't everything, as Omi soon learns.
Dojo's craving for Shen-Gong-Wu reaches the breaking point, which causes chaos for everybody. It happens every 1500 years, and Dojo must be locked in a cage for 24 hours to calm down. This doesn't last long, however, as Dojo tricks Omi and goes loose. Growing a second head, Dojo becomes evil and goes on a rampage throughout China searching for Shen-Gong-Wu.
After receiving a warning message from Omi in the future, the Warriors set out to find the time-traveling Shen-Gong-Wu, Sands of Time. In the message, future Omi explains that evil is ruling the universe, and the Sands of Time is the key to changing the future. Jack, however, beats them to it and uses it to travel back in time to recruit some of the world's ruthless villains. He also brings his future self into the present time, knowing that future Jack already knows the locations of all the Shen-Gong-Wu before they reveal themselves!
The Warriors are having trouble working together as a team. After finding the Mind Reader Conch, each Warrior uses it to see what the other thinks about them, which only continues their problems. Jack introduces his latest invention, the Molar 2000, which he uses to break into the Temple vault, stealing most of their Shen-Gong-Wu. The Warriors team up with Jack's visiting cousin, Megan, to try and retrieve what's rightfully theirs.
Using the newest Shen-Gong-Wu, Shadow of Fear, Jack enters the Warriors' dreams to bring their deepest and darkest fear to life. With no one guarding the Temple vault, Jack easily steals some Shen-Gong-Wu. Master Fung advises the Warriors that they must face their fear in order to ultimately overcome it. All the while, Jack directs a movie about his adventures with the Warriors.
Guan, one of the greatest warriors of all time, shows up and meets the Xiaolin Warriors for the first time. Guan tricks Dojo to accompany him to a palace where Chase Young, one of the most evil villains of all time, resides. However, Dojo doesn't know this. There, Guan trades Dojo to Chase in order to get his Spear of Guan back. Without the Spear, Guan is practically nothing. Dojo is horrified when he learns what Chase plans to do with him.
After Kimiko accidentally breaks the Mosaic Scale, she hides the pieces in Clay's room. The next day, Clay starts acting weird ... and acting up. It turns out that the Mosaic Scale was used to contain a mischievous spirit named Sabeeny, an earwig who has possessed the Dragon of Earth. If Sabeeny finds the Monarch Wings, the sister Shen-Gong-Wu to the Scale, and combines them with the Mosaic Scale, it will no longer need a host! The earwig will become invincible! Can the Warriors stop Sabeeny?
When the Heart of Jong falls into a crevice and is buried under a pile of snow while the Monks and Jack Spicer are trying to possess the Lunar Locket, the Shen-Gong-Wu's magic brings the pile of snow to life and Raksha is born. Wuya sides with him into bringing the Earth into a permanent Ice Age. Can the monks stop Raksha?
Every thousand years, the Shen-Gong-Wu form Mala Mala Jong on their own. Mala Mala Jong's new quest is to use the Ring of Nine Dragons to form into the Fearsome Four. Now, he travels to find the Emperor Scorpion in order to control all the Shen-Gong-Wu. Will the Warriors be able to defeat Jong once more?
The Warriors travel to Texas once again looking a new Shen-Gong-Wu but run into some trouble as soon as they get there. The Black Vipers, an all-girl motorcycle gang, capture the Warriors and keep them prisoner in a cave. Clay learns that one of the bikers is his sister, and that she's been holding a grudge against him their whole life. Can the Warriors escape unharmed?
After the Warriors befriend a mermaid trapped in ice that's being hunted by an ancient warrior, they soon discover that the warrior and mermaid aren't exactly what each appears to be.
The Warriors travel to Tokyo in search of the Zing Zom-Bone, a Shen-Gong-Wu that can turn anyone into a zombie-like state. Once there, they meet up with Kimiko's father, who is the owner of a major video game company. Unbeknowst to the Warriors, Kimiko's father brings in Pandabubba as his new business partner, not knowing he's in fact a criminal. Jack finds the Zing Zom-Bone first and brings it to Pandabubba who uses it on the company's workers and Kimiko's father to do his bidding. Can the Warriors stop Pandabubba a second time?
Upon seeing the rare Heylin comet circling the Earth, Master Fung orders the Warriors to not use any Shen-Gong-Wu for three days. The comet makes the Wu have a mind of their own if used by anyone. Wuya sees this as an opportunity to tempt the Warriors to use the Wu. After using the Golden Tiger Claws and Sword of the Storm to save his hometown from a volcano eruption caused by Jack and Wuya, Raimundo literally becomes attached to the Claws. The Shen-Gong-Wu begin to have a mind of their own and attach to Raimundo, making him 'monster-like'. Once Raimundo loses all his self control, Wuya plans to take over his body and finally carry out her plans to rule the world.
Upon watching Jack lose to the Warriors once again, Chase Young decides to help by having him steal the Tongue of Saiping and combine it with the Monkey Staff to control an army of green monkeys. After succeeding, Jack sends his army to fight the Warriors and ultimately wins, trapping them inside the Xiaolin Temple. Also, two new Shen-Gong-Wu are revealed, the Fountain of Hui and the Eagle Scope, that when combined, are able to reveal the greatest secrets of the universe -- and how to rid the world of evil forever. While the Warriors are trapped, Chase tries to find these Wu first.
Master Fung gives the Warriors their new and most important responsibility: guarding the Heylin seed from the forces of evil. But when they fail, they must find the Moonstone Locust to defeat the evil plant. Meanwhile, Vlad returns and forms a partnership with Jack.
After trapping Chase Young in the Sphere of Yun, Jack and his newest partner, Cyclops, take over his lair. He then proceeds to attack the Xiaolin Temple, stealing Shen-Gong-Wu from the vault. Omi later frees Chase using the Reversing Mirror, returning the 'favor' he owed him from earlier. The other Warriors do not know Omi freed him. Chase slowly tries to mold Omi into the true evil warrior he knows the young monk will become.
Chase Young is looking for an apprentice. Either KatnappÃ© or Jack will be able to win it. KatnappÃ© has reprogrammed the Warriors' U-bots to be evil. Master Fung informs the Warriors that their new threat is Chase Young, and he must teach the four monks to be deceptive in order to triumph. However, Omi is too trustworthy. After Chase chooses KatnappÃ© to be his apprentice, Jack turns to the Warriors and asks to join the side of good. Omi trains Jack the best he can to release all the evil that is inside of him, but after KatnappÃ© attacks the Temple, Jack takes off with the Warriors' Wu, which tests Omi's trust.
Jermaine returns and joins the Warriors as a Wudai Warrior, which is more advanced than a Xiaolin Apprentice. Omi is discouraged that Jermaine is ranked higher than him, and they constantly confront each other because of it. Jack soon learns that Jermaine's master is Chase Young, who doesn't know Chase is on the side of evil. Upon hearing this, the Warriors rush to notify Jermaine before it's too late. However, because of his encounter with Omi earlier, Jermaine refuses to listen.
After Jack inadvertantly releases the world's most biggest and powerful spiders, the Warriors, Jack, and Chase Young temporarily team up to stop the spiders before they proceed to consume the world. Kimiko, Raimundo, Clay, and Jack are captured while Chase and Omi escape. To look for an answer on how to defeat the spiders, they combine the Fountain of Hui and Eagle Scope. Will Omi and Chase be able to find the answer and put an end to the spiders' reign?
Master Fung tells the Warriors that one of them will soon advance to Wudai Warrior level, and each one is convinced that it is them. A new Shen-Gong-Wu is revealed, the Ying Yo-Yo, which acts as a portal to the Ying-Yang world. After losing the Wu, the Warriors learn that Master Fung has been taken and transported to the Ying-Yang world, but they cannot rescue him without the Ying Yo-Yo. Omi goes to Chase Young for help, who agrees to assist him. After finding the Yo-Yo, Omi enters the Ying-Yang world and rescues Master Fung, but upon leaving, Omi's good chi stays while his bad chi begins to take over . . .
With Omi gone to the dark side and Master Fung in an unshakeable meditative state, things look bad. They get worse when Chase Young uses the Serpent's Tail/Reversing Mirror combo to restore Wuya to her human form, albeit without her powers. Meanwhile, the Warriors minus Omi discover that it was Chase who sent Master Fung into the Ying-Yang world, and that unless you have the Yang Yo-Yo, your good chi will be trapped there. Master Fung apparently put himself in a meditative state to keep his evil side under control, but Omi wasn't so lucky. The Warriors and Dojo, with Jack Spicer tagging along, decide to retrieve Omi and Master Fung's chi from the Ying-Yang world . . .