After the Power Rangers participate in a charity skydive, a giant egg is unearthed at a construction site in Angel Grove. Lord Zedd and Rita Repulsa investigate the egg, and release the creature inside - Ivan Ooze, whom Zordon had trapped inside the egg six thousand years ago. Once released, Ooze leaves to seek revenge on Zordon, double-crossing Zedd and Rita by trapping them in a snowglobe. He disguises himself as a carnival wizard and gives free jars of ooze to children. Fred Kelman, the Rangers' young friend, accepts a jar, and brings it home. Later, his father finds the jar and inspects the ooze. When he pulls some out of the jar, mysterious charges of purple electricity go through him, putting him under the control of Ivan Ooze along with all of the other parents of Angel Grove. Apparently this ooze only affects adults, as it is later seen that the children and teens are not affected and are playing with the ooze.
When the Power Rangers are busy fighting Ooze's Ooze Men, the Command Center is left defenseless, allowing Ooze to enter and destroy it, leaving Zordon out of his time warp, dying. Due to the destruction, the Power Rangers lose their powers, and they must go on a quest to find new Ninjetti powers on the distant planet of Phaedos. When Ooze sends his Tengu Warriors after the Rangers, they are assisted by Dulcea, who bestows upon the Rangers new Ninja powers based on the six Ninja animals: the white Falcon, the red Ape, the yellow Bear, the blue Wolf, the pink Crane, and the black Frog. Dulcea directs the Rangers to find the Ninjetti Temple to find the Great Power on their own, as she will age rapidly if she takes one step off the plateau. On their way, they must battle a living dinosaur skeleton and at the temple battle four living statues. When the statues are destroyed, the Great Power is bestowed upon them and they morph into the Power Rangers again.
While the Rangers are away in Phaedos, realizing that the Great Power's potential, Ooze quickly uses this time to rush the workers to uncover the Ectomorphicon Titans at the site where the egg was uncovered. With all the parts unearthed, work to assemble the twin machines is completed at a factory. However, Fred manages to sneak into these 2 locations and discover Ooze's intentions.
When the Rangers return to Earth, they find it under attack by Ooze's Ectomorphicon Titans, and call upon their new Ninjazords to battle the Titans. They destroy Scorpitron, and then form the Ninja Megazord to battle Hornitor. During this time, Fred alerts the children of Angel Grove and makes them realize that Ooze plans to kill all of their parents. Fred leads them to the construction site where Ooze directed the adults to fall into a massive hole. When Ooze fuses with Hornitor, the Rangers form the Ninja Falcon Megazord to try and destroy him, eventually using Ryan's Comet, which happens to be passing the Earth, to destroy him. The Rangers struggle fighting Ooze, and Aisha has an idea: she hits a button next to her post, claiming that, "desperate times call for desperate measures", which causes the Megazord to knee Ooze in the groin, causing him to let go and come into contact with the Ryan's Comet, and destroying him and releasing the parents of Angel Grove from Ooze's spell. The Rangers get back to the Command Center, but Zordon has died. Tommy reminds the Rangers that with the Great Power, anything is possible. Combining their powers, the Rangers revive Zordon and restore the Command Center to running order.
The movie ends with a celebration in the Angel Grove harbor, thanking the Power Rangers for saving the world, although Bulk and Skull complain that it was themselves who saved the day. Later, during the credits, Goldar takes Lord Zedd's throne and jokingly proclaims himself king, just as the newly released (and presumably ticked off) Zedd and Rita walk in on him.