The movie begins with a karate tournament at Angel Grove's Youth Center. Competition in sparring has been eliminated down to two final contestants: Jason Lee Scott, the Red Ranger, and newcomer Tommy Oliver. Tommy quickly takes a 4-2 lead, but Jason battles back to end the match in a 4-4 draw. Jason is impressed with Tommy, as are Zack Taylor, the Black Ranger, and Billy Cranston, the Blue Ranger. Kimberly Hart, the Pink Ranger, also shows some interest in Tommy, a fact her best friend, Yellow Ranger Trini Kwan, is quick to pick up on.
The next day at school, Tommy stands up to Bulk and Skull, the school bullies, when they harass Kimberly. She is further impressed and invites him to a study date at Ernie's Juice Bar.
But Rita Repulsa, also impressed with Tommy's abilities, sends a squad of Putties to attack him while he is on his way to meet Kimberly. When he defeats them, she captures him and takes him back to her palace on the moon. There she coats his body with magical wax and casts a spell on him, brainwashing him into becoming her servant. He swears allegiance to his "empress", and she assigns him to destroy Zordon, the Command Center, and the Power Rangers. To fulfill the mission, she gives him the Dragon Power Coin, and he morphs into the Green Ranger.
The Evil Green Ranger goes first to the Command Center, which he can enter since he possesses the Dragon Power Coin. He finds Alpha 5 recharging, and inserts a CD-ROM containing a computer virus, causing the droid to convulse and stumble all over the Command Center. Zordon, who was in a meditative state when Tommy entered, demands that the intruder reveal himself. Tommy does, boasting of his newly acquired power. Then, despite Zordon's offer to help him break the spell, he breaks the dimension contact with Zordon, tearing the Command Center's computers to pieces and ripping up the circuitry.
In spite of the virus, Alpha manages to make contact with the other Rangers, who were cleaning Billy's car, the RADBUG. His erratic talking and the failure of the communicators and the teleporter mechanisms alerts the Rangers to the fact that there is something seriously wrong. They take the RADBUG to the Command Center, where they are shocked to find the place totalled, Alpha staggering around talking gibberish, and Zordon gone. Billy removes the CD-ROM from Alpha's system, rendering him semi-operational, and try to figure out what happened. But Alpha can tell them nothing, since the virus scrambled his memory banks.
Meanwhile, Rita uses her magic wand to grow Goldar to gigantic size. After a brief battle with some Putties, the Rangers summon their Dinozords, combine them into the Megazord, and draw the Power Sword to fight Goldar. Suddenly, Goldar disappears, and the Green Ranger breaks into Megazord's control center, kicking the other Rangers out to the ground below. He then single-handedly defeats all five Rangers in combat.
They return to the Command Center, stunned at the beating they took from this "guy in a green costume." Suddenly, Alpha lurches, falls forward, and shuts down; the virus is still in his system. Jason grimly warns the others that they have only been through round one of what will be a major battle. The Power Rangers then watch the Viewing Globe as Green Ranger vows their downfall.
In the Command Center, as the Rangers debate their options on how to deal with the Green Ranger. Billy and Trini finish repairing Alpha, eradicating the virus from his circuits. While the Blue and Yellow Rangers set to work repairing the computers, the others return to town.
Tommy returns to the earth with orders from Rita to stay put until she calls for him again. After she leaves, he encounters Bulk and Skull, who want revenge for the way he humiliated them earlier. They demand an apology from him. Tommy's eyes, glowing an evil green, shoot sparks at Bulk and Skull's feet, scaring them silly and causing them to jump into a dumpster for cover. After Tommy leaves, they both agree that Tommy needs his eyes checked, wondering what is going on with him.
Jason, his pride hurt from his encounter with the Green Ranger, is taking out his frustration on a punching bag at the Youth Center. Slowly it dawns on both him and Zack that it must have been the Green Ranger who wrecked the Command Center. Meanwhile, Kimberly, who goes to ask Tommy why he never showed for the study date, notices a change in Tommy's personality. He rudely tells her he doesn't need her to worry about him and that she is not the center of his universe. Kimberly is offended and brokenhearted, and she expresses her feelings to Zack. Zack tells her to forget about Tommy for the time being, since they have "bigger problems to worry about".
Back on the moon, at Goldar's suggestion Rita decides to put Tommy through one final test: if he can defeat another band of Putties using only his natural karate skills, he will be given the Sword of Darkness, a legendary weapon which Rita's forces used against Zordon's Rangers millennia ago. Rita wants to give him this weapon because, as Finster explains, it will allow Rita to maintain control of Tommy forever, provided the Sword is not destroyed. The only one who knows of its power is Zordon, and he is not around to tell the other Rangers to destroy it. Rita and her minions go down to earth together to watch Tommy battle the Putties. Tommy soundly defeats them, exceeding Rita and Goldar's expectations, and is rewarded with the Sword.
Later, Jason meets Tommy and tells him that a workout session between the two of them will have to wait due to an "emergency". Tommy says he understands, and Jason turns to leave. Then Tommy zaps Jason with his Power Coin and sends him to Rita's Dark Dimension. There the Red Ranger encounters Goldar, who has stolen his morpher. Jason finds himself in a desperate struggle to regain his morpher and stay alive.
Zack and Kimberly decide to go back to the Command Center in the RADBUG and rejoin Billy and Trini, who have by now repaired the computers and restored them to partial power. Attempts to regain contact with Zordon fail. The Rangers become highly concerned about Jason's disappearance. Jason continues his struggle to get his morpher back from Goldar, who beats him around with sadistic pleasure.
The Green Ranger reappears and taunts the Rangers. In Jason's absence, Zack decides that they will go into battle to try to learn his indentity. But with Jason gone and the Green Ranger armed with the Sword of Darkness, he dispatches them even more easily than before. However, they call on the Megazord and force him to retreat. Rita is highly annoyed by this setback until Squatt and Baboo remind her that Jason is still their prisoner. Jason is then shown at the mercy of Goldar, who has received orders from Rita to finish him.
While the Power Rangers attempt to find Jason and renew contact with Zordon, Jason continues his desperate confrontation with Goldar, trying to hide in the Dark Dimension's mist. Kimberly continues her search for Jason at Ernie's Juice Bar. When Bulk and Skull offer to help, demanding a kiss as payment, quick-thinking Kimberly tricks Skull into kissing Bulk! Leaving the dimwitted duo to argue with each other, Kimberly resumes her search and encounters Tommy. She tries to ask Tommy about Jason, but he replies that Jason didn't show up for a practice session they had scheduled, taunts her for being a worry-wart, and walks off. She and Zack go to ask Tommy about Jason again; but Rita, realizing that they might suspect him of being the Green Ranger, sends a squad of Putties to attack. This gives Tommy time to slip away. Zack and Kimberly wonder why the Putties didn't attack him, but suspect nothing.
The Green Ranger, his secret out of danger, gains Rita's permission to take Goldar's place in the Dark Dimension and kill Jason. Goldar leaves, jealous of being deprived of the honor. Words are exchanged between the Red and Green Rangers. The fight begins anew. Jason grabs his morpher, but before he can use it, the Green Ranger pins him to the ground and takes a moment to gloat over his victory. But just before he can strike the final blow with the Sword of Darkness, Billy, who has repaired the communicators and teleportation devices, finally isolates Jason's whereabouts and teleports him back to the Command Center.
Goldar, furious, harshly reprimands the Green Ranger, who begs for another chance. Goldar replies that he'll have to check with Rita and leaves the Green Ranger in the Dark Dimension for the time being. The Green Ranger undergoes further practice with his karate skills in preparation for another battle with the Power Rangers. When he does ask Rita for another chance, Rita tells him to be patient because the time is not right.
The reunited Rangers discuss Jason's experience, compare notes, and realize that Tommy isn't being honest with them, but they still don't draw any connection between Tommy and the Green Ranger. And they are no closer to finding Zordon.
Meanwhile, Scorpina, one of Rita's most dangerous minions, rejoins Rita after 10,000 years, and she is sent to attack Angel Grove. The Rangers do battle with her, further taxing themselves until she is recalled. While the Rangers recover in the Command Center, Alpha 5 finally finds a way to track down Zordon. He is beginning to renew contact when Rita sends a giganticized Goldar to attack the city, intending to force the Rangers to summon the Megazord, all the while cooking up a spell to cause a solar eclipse and drain the Megazord, energized by solar power, of it's energy. The Rangers then watch desperately on the Viewing Globe as Goldar destroys several buildings in downtown Angel Grove.
Realizing that they have no choice but to fight yet again, the Rangers draw their morphers. However, when they try to morph, sparks fly and the Command Center blacks out. Apparently, focusing the energy on finding Zordon drained power from the Morphing Grid, and nothing (morphers, Zords, communicators, and most of the lights in the Command Center) works. Goldar manages to tear a section of Angel Grove apart before Billy reconfigures the Command Center and restores power. The Rangers morph and go to fight Goldar.
After a short exchange with Scorpina, some Putties, and the giant Goldar, the Rangers have a brief confrontation with Rita. She sends Goldar to the beach, carrying a bus with Bulk and Skull, who were trying to flee the city, in one hand. The Rangers teleport after him, trying to save the troublesome duo. After a few tense moments of watching Putties pushing the bus toward a cliff, the Rangers call on their Zords, and the Megazord catches the bus just before it falls, depositing an overjoyed Bulk and Skull back on the cliff.
Meanwhile, Rita again sends Tommy, who has been practicing swordplay in the Dark Dimension, to the Command Center, this time to get rid of Zordon for good. He pulls the plug on Alpha, exchanges words with a partially restored Zordon, and then presses a few buttons to undo all of Alpha's work in bringing him back. He is just about to leave when, much to his surprise, Alpha reactivates. Having accessed his "backup power generators", the quick-thinking robot traps him in a force field. Unfortunately, all the progress made in finding Zordon is lost, to the dismay of Alpha and the glee of the Green Ranger. Alpha indignantly sets into motion a program to learn Green Ranger's indentity.
The Megazord, which is dealing a heavy beating to Goldar, suddenly finds itself fighting Scorpina as well, who has also been enlarged and now sports a hideous appearance. Furthermore, Rita's solar eclipse begins and drains the Megazord of its power, so that it is overwhelmed by the dual attack and knocked to the ground. Jason calls for the Power Sword to give the Megazord a power boost. It works, and the Megazord is immediately back on its feet when it grabs the sword, going on the offensive again. Rita, determined not to lose the fight, uses a spell to free Green Ranger from the Command Center force field (to Alpha's consternation), grows him to giant size, and sends him into battle as well. The Megazord is surrounded by Goldar, Scorpina, and the Green Ranger, and doesn't have enough power to finish the battle. Scorpina further weakens Megazord by electrocuting it with her stinging tail, while Goldar and the Green Ranger combine their swords to deal Megazord a crippling shockwave The Rangers are thrown out from the exploding Megazord, demorph involuntarily, and watch helplessly in shock as the defeated Zords fall into a crevice in the earth and are consumed by lava.
Back in the Command Center, all the Rangers except Jason are considering surrender, with Jason and Alpha 5 desperately trying to persuade them otherwise. But with the Zords totalled and the chances of finding Zordon under ten percent, there isn't much hope. However, Alpha does have some good news; while Green Ranger was trapped in the force field, the computer learned his identity. The Power Rangers then look into the Viewing Globe and react in utter disbelief upon discovering that their nemesis is, in fact, Tommy.
Upon discovering that Tommy is the Green Ranger, the Power Rangers are at first in shock and denial. But once they face the facts, they split up to find him, on a quest to save him from Rita's power.
Kimberly goes to the Youth Center and finds Ernie, Bulk and Skull watching the news reports of the last battle. Bulk and Skull are making ridiculous claims about being the ones who scared Goldar away; to this Kimberly responds, "Dream on!" Then she asks Ernie if Tommy is around, and he directs her to the weight machines where Tommy is working out. She tells him that she knows his Green Ranger identity. She is left speechless when he glares at her with eyes glowing green, addresses her as the Pink Ranger, and threatens to destroy her and the other Rangers and bring the world under Rita's rule.
Meanwhile, toasting her victory over the Megazord in her palace on the moon, Rita decides to complete the destruction of the Power Rangers by reviving the Dragonzord, dormant for 10,000 years. She gives Tommy the Dragon Dagger, and he assumes control of this new Zord and wreaks havoc on downtown Angel Grove.
The Rangers are discussing Kimberly's encounter with Tommy when Trini frantically bursts in and tells them about this new assault on their city. The Rangers morph into action, but without their Zords, they can do nothing to stop the Dragonzord.
As the Rangers fight a losing battle with Tommy, desperately trying to convince him that he doesn't know what he's doing, Alpha finally succeeds in his search for Zordon. When Zordon returns to the Command Center, he and Alpha revive the damaged Dinozords from their lava prison and return them to the Rangers. Zordon also tells Jason that he must destroy the Sword of Darkness to break Rita's grip on Tommy's mind. Rita, upon seeing the Zords resurrected, gets one of her famous headaches.
A one-on-one duel ensues between Tommy, controlling the Dragonzord, and Jason in the Tyrannosaurus. When the Dragonzord is beaten down, the Rangers call on the Megazord to finish it off. Megazord succeeds and hurls the Dragonzord into the side a mountain.
Once the Dragonzord is disabled, Jason, who has received orders from Zordon to destroy the Sword of Darkness to break the spell, leaps from the Megazord to fight Tommy in person. The Red and Green Rangers battle back and forth in an evenly matched duel. Green Ranger activates his golden chest armor, the Dragon Shield, to ward off Jason's attacks. Just when it appears Green Ranger will win, Jason finally throws his Power Sword at Tommy, knocking the Dragon Dagger and Sword of Darkness out of his hands. Green Ranger, unprepared for this blow, is thrown on his back. Jason draws his blade blaster, says, "It's all over, Tommy!", and shoots and destroys the Sword of Darkness. Rita's spell is broken, and Tommy involuntarily demorphs.
When Tommy revives, he is remorseful over what he has done. But Jason and the other Rangers are quick to forgive him, taking into account that he was under an evil spell, and Jason invites him to join the team as the sixth and final Ranger. Tommy is reluctant at first, but the others convince him that he belongs with them and can use his powers against Rita. At that, Tommy agrees to join the team.
From the Command Center, Zordon and Alpha watch what Zordon calls the fulfillment of a historic prophecy, that the Sixth Ranger would fight for justice rather than evil. Rita and her minions, meanwhile, are enraged that they lost the battle when everything was going so well for them, and Goldar promises vengeance.
Meanwhile, Zordon summons the six Rangers back to the Command Center. He praises Alpha for displaying leadership in his absence, and commends the five main Rangers for their refusal to give up when the odds were against them. He then confirms Tommy as the Green Ranger, and Tommy promises to obey the Rangers' three main rules. He also tells them that Dragonzord can go into Battle-Mode by combining with the Mastodon, Triceratops, and Saber-Toothed Tiger Dinozords. The movie ends with Billy presenting Tommy with his own wrist-communicator, Jason and Tommy shaking hands in friendship, and the six Rangers huddling up for a Power Ranger high-five.