Shane, Tori and Dustin are three students at the Wind Ninja Academy. Their less than stellar performance gets them the occasional lecture from their Sensei. One day, the academy was attacked by Lothor, a banished ninja master who has returned to capture all ninja students. Shane, Tori and Dustin are the only three remaining students, and along with Sensei and his son Cam, retreat into the underground Ninja Ops. There, the three are given morphers, which allow them to transform into Wind Rangers and protect the city of Blue Bay Harbor from Lothor's forces.

When Lothor demonstrated his ability to make his monsters grow into giants, the Rangers unleashed the Ninja Zords, which could combine into the Storm Megazord and destroy monsters with its arsenal of Power Spheres. Lothor again raised the stakes by sending his new allies to battle the Wind Rangers - the Thunder Rangers Blake and Hunter, who had their own Thunder Zords. The Thunder Rangers were on a mission to destroy the Wind Rangers' Sensei, who they beleived to be responsible for their parent's death, but a visit from the afterlife from Blake and Hunter's parents showed them the truth - that it was Lothor who killed them. The Thunder Rangers saw the error of their ways and joined the Wind Rangers in the battle against Lothor, bringing the Thunder and Ninja Zords together to form the Thunderstorm Megazord.