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.

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.

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.

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 . . .

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?

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.

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?