A new and powerful super-hero known as Firestorm attracts the attention of the Super Friends. They invite him to join their team, and he gladly accepts their offer. His powers are a great boost to the team when Darkseid, ruler of the planet Apokolips, comes to Earth and kidnaps Wonder Woman as his unwilling bride.
Darkseid has taken Wonder Woman back to his home planet of Apokolips to be his bride. The Super Friends and their new team-mate, Firestorm follow him to his home world, but find that Darkseid's minion, Desaad, has used a mind-controller on Wonder Woman. The Super Friends must avoid Darkseid's trap, and rescue Wonder Woman.
Brainiac joins forces with Darkseid, and creates android duplicates of both Superman and Wonder Woman that are powered-up by Darkseid's Omega Beams. They use the androids to attempt to capture the Super Friends. The team has use their skills to tell which Superman and Wonder Woman are the real deal, and then save themselves from Darkseid's plan.
The super-villain known as the Mirror Master uses his new invention to trap the Super Friends in the dimension inside of all mirrors. Together, the Friends must use all their resources to escape this trap, and stop the Mirror Master.
Luthor creates a power-transfuser to absorb all of the Super Friends combined powers into his own body. With his new super-abilities, and a new power-suit, Luthor attempts to rule over Darkseid, but is thwarted when Darkseid uses Kryptonite dust against him, that affects his powers stolen from Superman. With Luthor facing defeat, the Super Friends have to find a way of getting their super-powers back.
After stealing a magic lamp, an otherwise idiotic thief known as Benny the bungler is confronted by what he believes to be a genie. In reality, it is Mr. Mxyzptlk, and he grants Benny the power to commit super crimes. With the Super Friends clueless as to how a simple thief is committing these crimes, they have to find a way to stop him, and deal with the even more powerful Mxyzptlk as well.
The older members of the Super Friends, including Batman and Superman, are called away to outer space, to stop the destruction of a distant inhabited world. In the meantime, back on Earth, Robin, Firestorm and the Wonder Twins, together with the Hall of Justice itself, are shrunk down in size by Luthor's new ray. The young heroes must work together in order to free themselves from Luthor, and restore everything back to normal size.
Captain Mystery, a useless amateur super-hero, wants to join the Super Friends, but they decline his request. Afterwards, Luthor steals the computer controller disk from the Hall of Justice, and after setting up a trap for the Super Friends, Captain Mystery ends up being their only hope of defeating Luthor.
The last remaining chunk of Gold Kryptonite (which can remove Superman's powers forever) is being auctioned off by the Intergalactic Underworld organization. Three of the Super Friends including Wonder Woman, Firestorm and Black Vulcan, go undercover within the organization in order to be the highest bidders for the Kryptonite, beating Darkseid.
Wonder Woman, Firestorm and Black Vulcan have been captured by Darkseid after their true identities are exposed. Superman, Batman and El Dorado follow their companions to outer space. They end up competing on the Moon of Games, where El Dorado learns from Kalibak where Darkseid is holding their friends, and that he now has a small quantity of Gold Kryptonite. Superman and the remaining Super Friends must proceed carefully in order to save the others, before Darkseid can use the Kryptonite to stop Superman forever.
While transporting Professor Martin Stein (one half of Firestorm) and his new omnicaster in the Batplane, Batman and the plane crash-land on an island. The Super Friends go to the island to rescue Batman and Professor Stein, but encounter a reptile-man dinosoid calling himself Dr. Corwin, who has created a genetic manipulation beam that can change any animal into its dinosaur counterpart. Corwin has also turned Batman and Stein into reptile men, and after Wonder Woman is also transformed, the Super Friends must restore them to normal whilst fighting Corwin's dinosaur army.
The Wonder Twins accidentally expose Superman to the unpredictable Red Kryptonite, which this time turns him into a Super Brat. Mr. Mxyzptlk learns of these events and manipulates Super Brat into occupying the Super Friends' time. The Super Friends must bide their time whilst dealing with Mxyzptlk, and wait for the Kryptonite to wear off.
A villain called the Dollmaker uses his special magic mud to create dolls of the Super Friends. With these dolls, he then controls their minds and actions, forcing them to commit crimes on his behalf. With El Dorado not yet represented by one of the dolls, only he is left to free his team-mates and stop Dollmaker.
On the planet Tiron 7, Darkseid has enslaved the population and intends to use the planet as a testing ground for his new weapon that will transfer the entire planet into a negative universe. After responding to the inhabitants' plea for help, the Super Friends attempt to stop Darkseid's latest plan, and save the planet.
Apache Chef and the Wonder Twins go for a nature walk near the small town of Buzzard's Roost, where all the population is under a hypnotic suggestion. The Twins are then captured by the townspeople, and Apace Chief enlists the help of Wonder Woman to assist him. Together, they find out that it is Brainiac who is controlling the town, and they must stop him and his helpless slaves in order to free both of the Wonder Twins.
On an alien planet, Romlar, curator of the Galactic Museum, is stealing people and artefacts and buildings from all over the galaxy to fill up his museum. Eventually, he steals the Hall of Justice and several of the Super Friends from Earth. He places all of the stolen goods in suspended animation, and Superman and the remaining Super Friends journey to his museum to stop him from keeping all the people and artefacts frozen for all time.