The story opens with Emperor Ming the Merciless (Max von Sydow) declaring that he will first play with, and then destroy, the Earth, using seemingly natural disasters which include earthquakes, hurricanes, volcanic euptions, tornados, and something called "hot hail".
Sometime later on Earth, New York Jets football star "Flash" Gordon (Sam J. Jones) boards a small plane. Onboard, he meets travel journalist Dale Arden (Melody Anderson). Mid-flight, the cockpit is hit by a meteorite sent by Ming and the pilots are sucked out. Flash takes control, and manages to crash land the craft in a greenhouse owned by Dr. Hans Zarkov (Topol). Zarkov, who believes the disasters are being caused by an unknown source in space which is sending the moon toward the Earth, has secretly constructed a rocket ship with which he intends to investigate. Zarkov's assistant refuses to help him, so he lures Flash and Dale inside the rocket. After a struggle, the rocket launches into orbit, taking the trio through a vordex to the planet Mongo. There, they are taken prisoner.
Flash, Dale and Zarkov are brought to the palace before Ming. Ming orders Dale to be prepared for his pleasure. Flash attempts to resist but is overpowered by Ming's bodyguards. Ming orders Zarkov to be reconditioned and Flash executed by leathal gas. Ming's daughter, Princess Aura (Ornella Muti), manipulates Ming's Chief Surgeon into helping her save Flash, to whom she is attracted, by having him injected with an imunity seurum helps him escape from the palace.
Zarkov is seemingly brainwashed by Klytus (Peter Wyngarde), the golden-masked de facto regent of Mongo and Ming's right hand man. Meanwhile, Aura and Flash flee in a shuttle to Arboria, the kingdom of Prince Barin (Timothy Dalton), Aura's lover. En route to Arboria, Aura reluctantly teaches Flash to use a telepathic communicator to contact Dale. He uses it let her know he is still alive. Dale informs Flash that she is locked in Ming's bedchamber. Encouraged by Flash, Dale escapes. Klytus dispatches Zarkov to intercept Dale, who informs Zarkov and a listening Klytus that Flash is alive. The two then escape, as Zarkov reveals he was able to resist the brainwashing process. But after fleeing the city, Dale and Zarkov are captured by Prince Vultan's (Brian Blessed) Hawkmen and taken to his kingdom, Sky City.
Aura and Flash arrive at the forest moon Arboria. Aura asks Prince Barin to keep Flash safe. A distrustful Barin, who is in love with Aura, agrees not to kill Flash, but then contrives to force him to take part in a deadly ritual. Barin and Flash take turns sticking their hands into a hollow stump with a poisonous creature inside. When Barin compels Flash to take an extra turn, he pretends to be stung by the creature and begs for a quick death, using this as an opportunity to escape. Barin follows, but they are both captured by Prince Vultan's Hawkmen.
Back in Mingo City, Klytus informs Ming that Flash is alive and gains Ming's authority to discover the person responsible. Aura returns alone to Mingo City only to be taken prisoner and tortured by Klytus and General Kala (Mariangela Melato), the head of Ming's secret police. They force Aura to confess to helping Flash escape, and Ming orders her to be banished to the ice moon Frigia after his wedding.
Meanwhile, Flash and Barin are captured by the Hawkmen and taken to Sky City, where Flash and Dale are briefly reunited. Flash is forced to fight Barin to the death, but Barin joins forces with Flash when he saves his life. Klytus arrives and threatens Vultan as well as everyone else for their insolence. Flash and Barin double-team up to overpower Klytus and kill him. Knowing that this will bring retribution on the Hawkmen, Vultan orders them to evacuate Sky City, leaving Barin, Flash, Dale and Zarkov behind. Ming's ship arrives shortly afterwards and he orders Barin, Zarkov and Dale to be taken aboard. Ming finds himself impressed with Flash, and offers him lordship over a subjugated Earth in exchange for fealty, as an alternative to death, which Flash refuses. Ming returns to his ship and gives the order to destroy Vultan's kingdom with Flash still on it. Flash cheats death by finding a rocket cycle in the city and escaping before Sky City is destroyed.
Flash contacts Vultan, whose people have found refuge on Arboria, and they plot an attack on Mingo City. Flash pretends to attack Mingo City alone on his rocket cycle. General Kala dispatches the war rocket Ajax to bring back Flash's body, but the Hawkmen army intercepts and Flash and the Hawkmen seize control of the rocket after a fierce battle.
In Mingo City, Princess Aura overpowers her guard and frees Barin and Zarkov from the execution chamber. Flash and the Hawkmen attack Mingo City in Ajax and Kala activates the city's defenses, as Ming and Dale's wedding starts. Mingo City's lightning field sheild protecting the city can only be penetrated in time to save Earth by flying Ajax in to it in a suicide run. Flash volunteers to stay at the helm to ensure it is successful and allow the Hawkmen to invade the city.
Just before the rocket hits, Barin manages to kill Kala then then sabotage the lightning field generators and Ajax plummets into the city's great hall where the wedding is taking place; the ship's bow impales Ming. Ming falls off the rocket nose, seriously wounded, and Flash offers to spare his life if he will stop the attack on Earth, but Ming refuses to submit. Ming attempts to use his power ring on Flash but his power falters and nothing happens. He then aims the ring at himself and is seemingly vaporized by its remaining power seconds before the counter to the destruction of the Earth reaches zero.
A huge victory celebration ensues with planet Earth apparently saved and Barin is proclaimed the new ruler of Mongo. Vultan is named general of all of Mongo's armies including the Hawkmen. Thus Mongo's population can live in peace. Aura chooses to marry Barin and stand alongside him. Flash, Dale and Zarkov are asked to stay on Mongo for the time being since the vortex to Earth has been severed with Ming's demise. They all agree to stay, while Zarkov will plan on a way to get the three of them back to Earth somehow.
The final shot focuses on Ming's empty power ring, as an unidentified individual picks it up. The words "The End?" fade onto the screen, followed by an echo of Ming's evil laughter.