Kareem Azaar is a ruthless thief on the planet Zaghdad who has stolen the Magic Lamp of Olam, which contains the power of an evil genie. Kareem uses the Genie's power to take over the planet and banish the Sultan into the world of the Genie's lamp. When the Super Friends arrive to do battle, Superman and the Wonder Twins wind up in the lamp as well, leaving the other heroes to take on Kareem's forces.

While protecting a prehistoric planet from a meteor, Superman ends up hit by the meteor's nuclear core, crash lands on the medieval planet of Camelon, and loses his memory. A bunch of rebels led by Logan take him in as their black knight in a plan to overthrow King Arthur 7. It is up to the Super Friends to help Superman remember who he is and defeat the rebels.

What starts off as a camping trip for the Wonder Twins turns into a nightmarish adventure in Middle Earth when the Super Friends must battle a black magic sorcerer named Mal Havok who has taken over the troll kingdom. Mal Havoc uses his magic to turn the Super Friends into trolls. With their powers reduced, Batman and Wonder Woman accompany the troll king on a mission to free Middle Earth of the evil sorcerer.

In a parallel universe, the Super Friends are supervillains, the Super Enemies. Mount Vesuvius is a focal point that links the two universes — in one universe, Superman tries to stop the eruption, while his evil counterpart is causing the same disaster in his own reality. Vesuvius explodes, causing the two Supermen to exchange universes. While Superman has to fight his evil comrades and find a way back to his own world, his evil counterpart battles the real heroes and begins his plan to conquer Earth.

The evil Captain Nimoy plots to use nuclear warhead missiles to sink continents below the sea where he plans to rule. Nimoy is aided by an android duplicate of Batman to help him out, but with Superman and Wonder Woman away on a space mission, the Super Friends are aided by Superman's tiny Kryptonian friends from the bottle city of Kandor.

When a descendant of the original Dr. Frankenstein abducts and steals the powers of Batman, Superman and Wonder Woman and transfers them into his latest creation, it is up to Robin to stop the Super-Monster. He transfers the remaining powers into himself, then manages to restore the Super Friends' powers.

After the Wonder Twins and the Dynamic Duo find out they are not able to get rid of a tornado, the storm transports the Hall of Justice to the Land of Oz, where Mister Mxyzptlk, who has once again escaped from the Fifth Dimension, informs the Super Friends that they must find the Wizard to get home. Along the way, they encounter the Wicked Witch of the Worst Kind in a gingerbread house, who turns Aquaman into the Scarecrow, Superman into the Tin Man, and Wonder Woman into the Lion.