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?

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.

Chase Young is looking for an apprentice. Either Katnappé or Jack will be able to win it. Katnappé 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 Katnappé 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 Katnappé attacks the Temple, Jack takes off with the Warriors' Wu, which tests Omi's trust.

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 . . .

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.

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?

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.

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?

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.

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?