Omi, a young Xiaolin Dragon-in-training, is joined at the Xiaolin Temple by three new students, Kimiko, Raimundo and Clay. Initially, they don't get along at all. But when the ancient evil spirit Wuya is set loose after a thousand years of imprisonment, Omi soon learns to appreciate his new companions.

Everyone doubts Clay's competence. But when Omi, Kimiko and Raimundo are trapped in a magic box, it's up to Clay to save the day, which he does in his own slow and steady style.

Wuya uses Raimundo to steal Shen-Gong-Wu from the other three Chosen Ones. What then happens, she uses the Serpent's Tail & Reversing Mirror (a Shen-Gong-Wu that reverses the effects of another) to become human once again...

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...