At STAR Labs, Professor Hamilton has discovered a hidden compartment inside the space craft that bought Superman to Earth as a baby. Inside is a strange looking device that resembles some kind of alien movie projector. As Superman and Hamilton examine the device, they notice that it has a viewer attached. Inside they see a hellish red limbo, where beings float by wraith-like. Superman identifies this as the Phantom Zone, a pocket dimension used by his people, the Kryptonians, to lock away their worst criminal offenders in lieu of the death penalty, which he saw in the Orb containing all of Krypton's knowledge that he retrieved from Brainiac. The Professor pushes a button and accidentally releases a large flying monster from the Zone that Superman has to wrestle to the ground for the Professor to send it back. After that's over with, the pair hears the disembodied pleas of a woman asking to be released from the Zone, as she has served the duration of her sentence. She tells them that her name is Mala.
Superman goes to his Arctic Fortress and accesses the Brainiac Orb, asking it to tell him everything about Mala. It seems that Mala was in charge of Krypton's planet-wide defense system, and was second in command only to General Jax-Ur. Jax-Ur became mad with the lust for power, and orchestrated a vicious overthrow of Krypton's Ruling Council with Mala by his side. Their coup was foiled by a young up-and-coming scientist, Jor-El, Superman's father. Jax-Ur pleads guilty to all the crimes and said Mala, as a career soldier, was only following orders. Jax-Ur was sentenced to an eternity in the Phantom Zone, while Mala was given 20 years. Since her term is in fact overdone, Superman decides to release her.
Superman and Professor Hamilton use the Projector to release Mala from the Zone. Superman introduces himself as Kal-El, and tells her that she was imprisoned for so long because Krypton was destroyed. She is disoriented and Hamilton tells Superman he can take her to STAR Labs' cabin retreat in the mountains until she gets her bearings. Superman picks her up and flies off. Mala is stunned and asks if all people on Earth can fly. He tells her that only he can, and that eventually she will be able to as well, once she absorbs enough yellow solar radiation. Superman spends the next several days in the mountains with Mala, teaching her how to use her developing powers, but making her promise never to injury a human as they are much more fragile. After a while, Superman decides to take her into Metropolis to assist him in his work as Superman.
That night, Superman and Mala spot some criminals robbing a bank. Mala likens them to insects raiding a nest. When the criminals split up, so do they and Mala proves to play a little too rough with humans without supervision. When the police arrive along with reporters, including Lois Lane, Mala makes a proclamation to all, promising to follow Superman's example of "Just rule, with a fair hand."
The next day, Mala is back at the cabin, alone and watching TV. Lex Luthor comes on, saying that now the truth comes out, that Superman and Mala fancy themselves Earth's masters, and that no doubt they will breed an army of Kryptonians to conquer the world and reduce the human race to slaves or pets. Mala likes the idea. Luthor goes on the say that if Superman really does care about humanity, then he should send "that criminal" back into the Phantom Zone. Mala goes blind with rage, destroying the TV and screaming that she will never go back! After calming down, Mala flies to STAR Labs and overhears Superman and Hamilton talking about her. Superman is giving Mala the benefit of the doubt, but tells the Professor to have the Projector ready in case Mala doesn't straighten out.
That night, at the Daily Planet, Mala and Superman are giving Lois an interview. Mala clarifies that she mistakenly thought Superman was in charge, but that she has no desire to conquer the world. Lois asks if she and Superman are an item, which Mala confirms. Superman assures Lois that it's nothing like that. Mala becomes upset, and accuses Superman of spurning the last woman of his kind for a lower creature like Lois. Superman tries to stop Mala from killing Lois, and the two battle. Mala says that she will kill every living thing on Earth before she goes back to the Phantom Zone, and judging Superman's response, realizes his problem is that he was raised as a human, so that he actually cares about them. She says if Jax-Ur were here instead, he would have conquered the Earth ages ago. She destroys a building knowing that Superman will have to save it in order to escape. After Superman does so, he hurries to STAR Labs only to find that Mala has torn through the place and taken the Projector.
On a field outside of the city, Mala activates the Projector and releases General Jax-Ur onto our world, assuring him that he will love it here... to be continued