While being pursued by Darkseid in space, Superman, Firestorm, and Cyborg take shelter in a gigantic space ship. They discover a female being who seems to cast her image all over. She is a princess who uses holograms to scare pirates away. Her planet was destroyed and she keeps the population of her people in her locket. Darkseid learns of this and plans to steal the locket. Superman's powers are cut in half due to the orange sun in the galaxy they are in.

Bizarro #1 decides that Bizarroworld needs more heroes than just Bizarro Supermen so he takes a duplicator ray to Earth and finding the right three heroes, he makes Bizarro duplicates of Wonder Woman, Firestorm, and Cyborg. All Bizarro #1 wants to do is take them back to protect Bizarroworld, but Mr. Mxyzptlk has other plans when he arrives on Earth and wants to have fun. He insists that before Bizarro #1 takes them back, they need training as Super Heroes and with their backwards minds, they wreak havoc on Earth. The Super Powers Team realizes that they will have to get rid of the imp in order for the Bizarros to go home.

The Super Powers Team has to search for Col. Steve Trevor, Wonder Woman's love interest who vanishes, but he shortly reappears and returns to Earth with no one knowing that Col Trevor has been captured and replaced by Darkseid who uses a molecular reconfigurator to impersonate Col. Trevor. The masquerade is to get a hold of the TC7 satellite, which Darksied plans to use as part of his plan to mutate the Earth and take it over. As a bonus, Darkseid also abducts Wonder Woman. So our heroes have two people to rescue and a satellite to retrieve.

The Scarecrow is plaguing Gotham City with his fear transmitters, but he has to contend with Batman and Robin, Gotham's Guardians. Batman has always been known as the man with no fear, but when he chases the Scarecrow into a certain alley, he is paralyzed with terror. The alley is none other than Crime Alley where years ago, Bruce Wayne witnessed the murder of his parents and guided his destination to becoming Batman. The Scarecrow plans to take advantage of this and captures Robin and Wonder Woman and uses them as bait to set a trap for Batman. The Caped Crusader now has to not only battle the Scarecrow, but his own fear as well.

A new villain called Ace recruits four young thieves and turns them into Super Villains called the Royal Flush Gang. With their new powers, they are able to capture Superman, Wonder Woman, and Firestorm. Ace is in cohoots with Darkseid, and things really get wild when Batman, Robin, and Cyborg raid their hideout. Batman also discovers that Ace is really his arch foe, the Joker, a rather unlikely foe to team up with Darkseid.

While attending a science fair with Ronald Raymond (Firestorm), Cyborg is captured by robots and is taken to a starship owned by Brainiac who uses Cyborg as his latest experiment. When Superman and Firestorm arrive, they have to battle a giant robot that Brainiac built to destroy them and Brainiac has transferred Cyborg's mind into the robot.

Felix Faust uses his magic to steal Superman's powers to transfer them to himself. But his cellmate, the Penguin jumps in the way and acquires them for himself. While the Penguin keeps the Super Powers Team busy with his super powered crime wave, Felix Faust conjures up spirits to capture the bird and get the Man of Steel's powers for himself.

Darkseid sees great opportunity to take over Star City, the first city in space built by Japanese billionaire Industrialist Dr. Moko. When Batman, Samaraui, and Firestorm journey up to the city, they and Moko's daughter are unaware that Moko has been captured and replaced by a robot duplicate. Meanwhile, Superman and Wonder Woman join Aquaman who has found an odd island which is not only Darkseid's base of operations, but a trap set for them. Batman, Samaraui, Firestorm, and Moko's daughter are forced to flee through Star City with the robot workers being contolled by Kalibak and Desaad. Their only chance is to cut off the power and black out the city.

The entire Super Powers Team as well as the entire world gathers to grieve over the tragic death of their most powerful hero. Superman has died due to an over exposure to Kryptonite while on a space mission. Firestorm, who was with Superman at the time is hardest hit and most vulnerable. Darkseid captures him and forces the details behind Superman's demise. Meanwhile, some of the heroes journey to the Fortress of Solitude to sort through Superman's things and they learn from one of the robot guards about a Kryptonian trance and that Superman may still be alive, which is great news considering Darkseid has taken over the Hall of Justice and has captured the rest of the Super Powers Team.