From the edge of the Milky Way, a winged creature named Rokan speeds toward Earth. Superman confronts the beast and realizes it is Rokan, a beast from Krypton which was thought to be extinct, and since Rokan is from Krypton, she has the same powers as Superman. Escaping, the creature wreaks havoc on Earth. The Super Friends attempt to stop Rokan by chasing her and her babies away with kryptonite.

Lex Luthor forms a criminal gang called the "Legion of Doom" and uses a dream-machine to make the Super Friends commit crimes. When the Super Friends are forced to turn themselves in to police headquarters, the guards reveal themselves to be Bizarro and the Cheetah, who send the Super Friends to the sun. The Legion of Doom then uses the Justice League satellite with Luthor's mutation device to turn women into Cheetah clones and men into Bizarro clones, long enough for them commit profitable robberies. The Super Friends return to Earth to reverse the damage done and retake The Hall of Justice. They then disguise themselves as Bizarro and Cheetah clones to stop the Legion of Doom.

The Wonder Twins agree to help Exxor defeat Darkon, a conqueror who has taken over Exxor and made its inhabitants his slaves. With the Wonder Twins captured by Darkon, Batman and Robin must free the twin heroes as the other Super Friends tackle Darkon and his troopers.

Captain Cold recruits the Fearians (inhabitants of Venus) to help the Legion of Doom take over the world and destroy the Super Friends. The Fearians say that the Legion has to make the environment suitable for Fearian life forms first, so Captain Cold freezes the world. When the Flash defrosts it, great quantities of steam make the temperature higher. Black Manta sets fire to an island in the Pacific Ocean. When Aquaman uses a great tidal wave to put out the flames, the water floods inland, making more plants grow. And finally, Sinestro sends six comets to Earth. When Green Lantern moves Earth out of its usual orbit to save it, the temperature rises even higher. The Fearians can now enter Earth to make it "Venus II".

While sailing with Captain Pierre Marcel, the Wonder Twins and Gleek get sucked in a whirlpool. After receiving a distress call from the Wonder Twins, the rest of the Super Friends search for the twins, only to get pulled in the whirlpool themselves. They emerge in a Wonder Land that is below the Earth's crust. The Super Friends must now search for the Wonder Twins and rescue them.

The World's Deadliest Game: Brainiac uses a cloaking device to make the Earth appear to vanish. When Wonder Woman, Hawkman and Black Vulcan are in deep space trying to find it, the Toyman sends a phony distress message that leads them to his sinister black hole planet of toy traps. The Riddler then uses his super-riddles to lead the other Super Friends on a wild goose chase that sends them to their doom. However, the efforts of Superman and Green Lantern foil their attempt and save Hawkman, Black Vulcan and Wonder Woman.

Traveling from space, three pirate ships make their way towards Earth. When Captain Sinbad and his Space Pirate crew reach Earth they start stealing treasures from South America. After receiving a message on the Justice League TroubAlert, Superman and Wonder Woman confronts Captain Sinbad and his Space Pirate crew. Captain Sinbad then hurls city buildings toward a mountain range allowing the pirates to escape the two Super Friends. The Super Friends regroup to strategize and later streak off to confront the Space Pirates. While trying to stop a Space Pirate boat, Wonder Woman gets hit with a stun laser and taken captive aboard one of the ships. Meanwhile, at the Hall of Justice, the JLA satellite monitor picked up Wonder Woman, causing Zan to convince Jana to go after her. When Zan and Jana find Wonder Woman, they get trapped by the Space Pirates and a mind-controlled Wonder Woman and are made Sinbad's slaves.

Gorilla Grodd invents an inter-spacial time conveyor to allow anyone to travel through the time portal. Black Manta and Giganta trap Aquaman and Apache Chief in 70,000,000 BC and rob the diamond mines of South Africa. Sinestro and Captain Cold trap Green Lantern and Samurai in AD 500 and rob King Arthur's treasure. Grodd and Solomon Grundy trap Batman and Robin in ancient Rome and rob the treasures of Julius Caesar. The Legion of Doom learn a hard lesson in underestimating the Super Friends when they are foiled once more.

Traveling from a distant corner of the universe, a fleet of unidentified ships head towards Earth to hypnotize all children and gather them to Monument Valley, Arizona. The Super Friends start to take action after the Wonder Twins became hypnotized and a call from the Justice League TroubAlert. After the Super Friends tried to stop the children from entering a spaceship, a UFO arose to destroy a nearby city. Batman and Robin stayed with the children as Superman and Wonder Woman stopped the UFO and the disasters it caused, only to get trapped inside the space craft as it heads to the Anti-Matter Universe. Meanwhile, at the Hall of Justice, the Wonder Twins escape by using hypnotic mind control on Aquaman to release themselves. Batman and Robin arrive back at the Hall of Justice to stop a nearby power source overload and snap Aquaman out of a mindless slumber.

Batman, Robin, Wonder Woman and Green Lantern guard the liquid light in the Astro-Chemical Research Plant. However, the Cheetah secretly steals Wonder Woman's Lasso of Truth, Brainiac steals Green Lantern's power ring and the Scarecrow steals Batman and Robin's utility belts. The three villains escape, and the Hall of Doom captures and puts the four heroes on a kangaroo court trial. Sinestro uses the power devices stolen by the three villains as evidence to prove the Super Friends are guilty. Brainiac punishes them by making them fight his android duplicates of them, and the captured Super Friends must save themselves from their own devices before it is too late.

In the remote heights of the Transylvania Alps, Dracula awakes after a 100-year sleep. Dracula starts havoc by releasing a strange glowing powder that turns people into vampires. Meanwhile, Batman and Robin receive a distress call and speed off to Transylvania. They search Dracula's castle, only to get captured by Dracula himself. Later Wonder Woman and Aquaman arrive in Transylvania after the Wonder Twins report it was taken over by bats, only to be attacked by dozens of mindless vampires. Another report of vampire attacks was made and this time Superman went to Vienna to stop them. While in Vienna, Superman runs into Dracula, who was continuing his plans of conquest, and gets turned into a vampire.

Solomon Grundy convinces the Legion of Doom to find the "Monolith of Evil" which gave him his powers where it revived him from his death. But when he, Grodd, the Cheetah and the Riddler cannot retrieve it, the Riddler tricks the Super Friends into fetching it for them by using a mirage to make it look like the Legion of Doom shrunk the United Nations building. However, they are in for a surprise when the Super Friends learn the truth of the Monolith's powers. They use it to put the Legion of Doom in their place — as the Monolith itself is not inherently evil, but acts upon the thoughts (evil or good) of whoever controls it.

After an experimental satellite from Kennedy Space Center falls back to Earth it breaks, releasing deadly radioactive energy. The Super Friends then receive a distress call from the West Coast saying Death Valley is being overrun by giant desert beasts. Wonder Woman and the Wonder Twins stay behind to check the Justice League computer for more information, while the rest of the Super Friends head to Death Valley. At Death Valley they find wreckage and a man who says giant lizards had nearly destroyed the town. As Superman continues to search for the mysterious giant beasts, he stumbles upon some mutated giant earthworms that he must save some teens from.

Bizarro has created a "giant ray" device that can turn anyone into 100-foot giants and uses it with the Justice League computer to transform himself, Sinestro, the Toyman and Captain Cold into giants. Each of them take over a continent of the world. But there is one catch: the Super Friends, after being helplessly hurled to Saturn, escape from their imprisonment and find out a way to use Bizarro's ray to stop them. Bizarro did not count on the Justice League's computer analysis that Bizarro thought the Super Friends would never be able to return. They unknowingly left traces of elements used by the device to turn Superman, Batman, the Flash and Green Lantern into 100-foot giants to combat their foes.

Three Kryptonian villains from the Phantom Zone escape and expose Superman to red kryptonite causing him to age rapidly. The rest of the Super Friends get trapped by the villains and only Superman can free them from the Phantom Zone. Meanwhile, the Justice League Computer tells Superman the only possible antidote for his rapid aging is blue kryptonite. Since blue kryptonite is harmful to Bizarro, it may have an opposite effect on Superman. Superman must take the Supermobile to go to the site where Krypton blew up and get the blue kryptonite in time to save the other Super Friends. Using the ray device the three villains stole from Superman, he sends the Kryptonian villains back to the Phantom Zone.

Lex Luthor has discovered the origins of Superman, Wonder Woman and Green Lantern. He proposes for the Legion of Doom to travel back in time and prevent them from existing. The Cheetah cheats in a tournament and becomes Wonder Woman. Lex Luthor becomes Green Lantern. The Legion of Doom alter baby Kal-El's spaceship away from Earth. However, after taking the other more obscure Super Friends prisoner, Batman, Robin, the Flash, and Black Vulcan find a tape of the plan that was carried out and uses the Justice League computer to find gaps in its memory, confirming that history was altered. They travel back in time, rectify Luthor's meddling and gain back their teammates.

In this story the Super Friends have to stop an energy draining monster which exists on computer tape and can appear anywhere at any time. Wonder Woman and Superman, during one scene, go undercover as a science expert and Clark Kent, in an attempt to learn how the energy creature can be destroyed. One of the scientists working in the lab turns out to be the culprit responsible for unleashing the energy creature. The story borrows heavily from the national headlines of the time during the concerns of a looming energy crisis.

Gorilla Grodd attempts to take over Gorilla City (a society of super-intelligent gorillas of which he is one) with a mind-altering vapor that induces fear in its inhabitants. However, King Solovar has protected himself from the vapor and has Grodd banished as he was before for attempting to overthrow him. Brainiac has created a brain-wave amplifier to control anyone in a 100-mile radius. Grodd convinces him to use it to take over Gorilla City. Solovar escapes before its activation and asks the Super Friends for their aid in stopping the Legion of Doom, who now control all the inhabitants of Gorilla City and wreak havoc upon an unsuspecting Africa.

The Super Friends must stop the plans of a conqueror named Torhana who seeks vengeance on the people of the surface world by freezing everything in his path. Torhana and his crew travel by ship, freezing oceans and continents and people...

The Legion of Doom makes a deal with an old swamp sorceress and her demon — an equivalent amount of the power of good in exchange for an equivalent amount of the power of evil. In order to gain that power of evil, the Legion decides to give the demon the Super Friends as the power of good. The Super Friends are captured and put to sleep in coffins. However, in the Legion of Doom's greed for more power, they capture the demon, believing he would give them an infinite source of power, and pay the price for it when he uses his powers to escape. Offended by this, he summons his army of zombies to attack them.

While in space, Batman and Superman become possessed by brain creatures. The brain creatures ultimately take over the minds of Wonder Woman, Robin, and Aquaman when it appears that the Wonder Twins are successfully defeating Batman and Superman's asteroid attack of Earth. atman and Superman, while under mind control, continue to attack Earth by firing huge asteroids on the surface.

The Legion of Doom has suddenly started acting heroic, much to the shocking surprise of the Super Friends. When a distress signal is transmitted to the Justice League computer, the Legion of Doom (acting as the Legion of Good) offers to help instead, but this proves to be a ruse in order for them to travel in time to the year AD 3984 to finally conquer Earth, aided by a savage group of futuristic mutants. With the Riddler leaving cryptic clues easily broken by Batman, the Super Friends learn in a much further century about their takeover and travel to 3984 to foil them.

A crooked space circus proprietor, Zarnum, uses a device to turn protected animals that have been illegally captured into beasts to boost attendance at his space circus. Sensing that the Super Friends are on to his scheme, he uses the device to change Wonder Woman, Aquaman, and the Wonder Twins into space creatures. It is up to the rest of the Super Friends to track down the elusive space circus, rescue the captive Super Friends, and bring an end to the poaching that has been taking place.

Superman, Batman, Wonder Woman, Aquaman and Apache Chief — as well as their sinister adversaries — are sent to another universe to engage in a series of contests where the losers will be eliminated. The other Super Friends and Legion of Doom members search for their missing colleagues.

Batman and Robin head off to a planet named Texarkana after receiving a distress alert that a local villain, the Capricorn Kid, is terrorizing the planet. After defeating the Kid and putting him in jail, the Kid vows revenge. He and his group of outlaws travel to Earth, break into the Hall of Justice, and plot their revenge on all the Super Friends. The Kid's group successfully places each of the Super Friends in dangerous situations and they deliberately force Batman and Robin into freeing each person...but the catch is that each trap is timed and the object of the game is to free all the Super Friends from the various traps before it is too late. In a showdown, Batman and the Kid meet up in an old-fashioned shootout.

The Toyman develops a device that can project anyone into the pages of a storybook. He forces Hawkman to chase him into Jack and the Beanstalk, the Cheetah forces Wonder Woman to chase her into Alice in Wonderland and Brainiac forces Superman to chase him into Gulliver's Travels. The three villains trap the three Super Friends in the treacherous books. However, when Batman, Robin, Green Lantern and Black Vulcan catch on, they trick Sinestro, Giganta and Captain Cold into helping them rescue their teammates by claiming that their fellow Legion of Doom members are still trapped inside the books.

At the start of the episode, the Super Friends are involved in an intense outer space battle. Moments into the battle, Wonder Woman gets a telepathic message from Aphrodite to help save the planet from a disturbance. Afterwards, all of the Super Friends show up and Aphrodite praises them on their great work and good will. An envious Hera gets into an argument with Aphrodite on Mount Olympus, which triggers the wrath of Zeus. Hera criticizes Aphrodite for praising "mortals" such as the Super Friends and she suggests to Zeus that the Super Friends are not as powerful as Aphrodite claims.

The Legion of Doom deserts Sinestro, Black Manta and Cheetah after a failed mission. The three villains decide to kill the Legion of Doom for their betrayal, until the Super Friends find out this is just a ploy to get them distracted.

Aquaman is exposed to a radioactive substance that turns him into a prehistoric sea creature from which he evolved. In order to cure him, Superman and Wonder Woman, inside the Supermobile, are shrunk down to microscopic size and sent within the creature's veins to attempt to give it another dose of radiation in the hopes that it will reverse the effects of the radiation and return Aquaman to normal. In the meantime the rest of the Super Friends have to do whatever they can to limit the creature's destructive nature all over the city.

The Super Friends mourn the death of Batman (a.k.a. Bruce Wayne) and have gone into hiding after the Legion of Doom unearth a crystal called "Noxium", created by one-time member Dr. Natas. The crystal emulates the weaknesses of each member of the JLA such as kryptonite, Yellow Power and lethal energy. It can then kill all of the Super Friends. The Legion of Doom then plans to take over the world after they have disposed of the Super Friends and the crystal, only for it to be found and disposed of in deep space, allowing the Justice League to stop the Legion, who finds out too late they were in hiding and had really killed off their android clones.

The Super Friends are visited by Mister Mxyzptlk, who comes complete with a script for a movie that he wants the Super Friends to star in whether they want to or not. The imp uses his Fifth Dimensional magic to cause the Super Friends to act out the script...but Superman is not affected by it. He nonetheless goes along with everything in an elaborate plot to trick Mxyzptlk into saying his name backwards — by using his heat vision to change the last word on the script.

The Earth is in ruins after an unexplained catastrophe occurs. Both the Super Friends and the Legion of Doom have been destroyed, as well as the human and animal population of Earth, rendering it dead.