Now with the world under his rule and Omi one of his many jungle cats, Chase is all-powerful. The world is in jeopardy, and it's up to the monks, Dojo and Jack to restore peace. The invisible creature that escaped the Ying-Yang world turns out to be the Chi guardian, who is out to retrieve every chi that was taken. After the creature takes Kimiko, Raimundo and Clay's chi, Dojo and Jack devise a plan on getting it back along with trapping the Chi guardian back in the Ying-Yang world. Once the Warriors' chi returns, they challenge Chase to a showdown in order to finally bring Omi back to the side of good.
The monks are now Wudai warriors, and they are going on their first Wudai quest. They received an omen from the singing old lady that the Bird of Paradise is coming. Their quest is to find the Bird of Paradise using a mystical leaf and using no Shen-Gong-Wu, they must search for the bird in Chase Young's domain. Using their new Wudai powers they've overcome obstacles that Chase Young has put in their way. When the warriors found the bird, they met with Chase and had a battle. At the end of the battle Jack appeared and took the bird. For our warriors, they were sad. Chase and Wuya left. And the same singing old lady comes back... What is the lady going to say to our warriors?
A new Shen-Gong-Wu, the Moby Morpher, has been revealed. Kimiko manages to get it, but it is soon stolen by the Ying-Ying Bird. The bird takes it to Hannibal Roy Bean -- the villain who turned Chase Young evil -- in the Ying-Yang World. Hannibal Bean then tricks Jack into freeing him from the Ying-Yang World, and now Bean plans to unleash a new type of evil on the world. Is this the end?
It is Chinese New Year and everyone except Omi receives gifts from their families. In an effort to cheer him up, Master Fung suggests Omi go on a quest to find where he belongs. The Warriors travel to a town where everyone looks exactly like the young monk. There, Omi finally finds his 'parents', though they are not exactly what he expected. Much to his fellow Warriors' dismay, Omi decides to stay with them on their farm. Now with one less warrior at the Xiaolin Temple, Wuya, Hannibal Bean and Jack plot to break into the Temple to steal Shen-Gong-Wu ... However, they do not know that they are being closely watched.
Master Fung sends the Warriors on a quest to find the Treasure of the Blind Swordsman. While on their quest, the Warriors will locate their new Wudai Weapons, each chosen for a particular monk. However, with Wuya and Jack hot on their trail, and Hannibal Bean secretly plotting something of his own, will the Warriors be able to succeed?
A new Shen-Gong-Wu is revealed, the Rio Reverso! A Wu that can change any object into its original form. Jack goes after it and with some help from Wuya Jack receives the Rio Reverso. Jack plots a plan to make an army of baby Dinosaurs made from oil. Wuya steals Jacks Rio Reverso and Wuya steals Jacks idea of an army of Dinosaurs and she ends up creating an adult T-Rex. How will the Wudai Warriors face this Dinosaur?
In preparation for going up against Hannibal Bean, Master Fung sends the Warriors and Dojo to a new temple, which turns out to be run by Master Monk Guan. Due to the arduous training and hostility with Guan, Raimundo quits and seemingly joins Hannibal Bean.
With the Shadow of Fear and Sapphire Dragon, Hannibal Bean enters Raimundo's mind to bring out his worst fear and use it against him and the monks. While they are busy fighting his fear, Bean puts his plan into motion to try and slowly break down Raimundo....but soon finds out things may not turn out the way he expected.
After learning a con dragon named Chucky Choo sold fake Shen-Gong-Wu to them, Wuya, Jack, and Cyclops vow revenge on him. Will the monks and Dojo be able to protect the misguided dragon? Or will Dojo and Chucky's past get in the way?
Hannibal Bean gets into Omi's head while he is sleeping and tells Omi that he should take all the Wudai Warriors elemental Shen-Gong-Wu and master the power of the elements to become the Xiaolin Leader. The whole thing was a set plot for Hannibal Bean, now will Hannibal Bean destroy Omi and take his elemental powers, or can Omi stop Hannibal Bean before it's too late?
Kimiko uses her PDA, the Mind Reader Conch, Changing Chopsticks and the Eye of Dashi to connect herself to a satellite so that she can read the world's thoughts. Hannibal Bean spies on her and acquires secret information about Chase's weakness by the Heylin Eclipse. Wuya teams up with Hannibal in an effort to destroy Chase and steal all the Shen-Gong-Wu.
Master Fung tells the monks that the leader will be revealed after they do their last quest. Omi decides to go back in time and stop Chase from entering the Heylin side. Realizing that he needs the Sands of Time, Omi freezes himself for 80 years in order to talk to his old self.
Omi successfully switches Chase Young's evil soup with pea soup which stops him from going evil. However, in exchange, the future changed for the worse. Hannibal turns Master Monk Guan evil instead of Chase, Master Fung is trapped in the Ying-Yang world and Jack turns good. After acquiring the soup Omi hid in the past, they are captured by Hannibal and his crew. Chase then sacrifices his good side to free the Warriors. After the Warriors get to the Heylin seed's vault (where Omi is frozen), Hannibal and his crew start a Xiaolin Showdown. Can the new Warriors defeat Hannibal, Wuya, Chase Young and Master Monk Guan in a 4-way tag team Xiaolin Showdown? And finally, who will be made the new leader?