A brief recap shows how Superman and Professor Hamilton discovered a Projector inside Superman's space ship that can send things to, and retrieve them from, the Phantom Zone. Superman chooses to honor Kryptonian Law and release a woman named Mala, an insurrectionist who has served her sentence. After Mala proves too dangerous, Superman is forced to consider sending her back into the Zone, but she beats him to the punch by stealing the Projector and, unbeknownst to Superman, releases her leader, General Jax-Ur!
This episode opens with Superman taking Professor Hamilton to his Arctic Fortress to view the schematics for the Phantom Zone Projector, stored in the Orb Superman took from Brainiac, in hopes of building a replacement. Once inside, Hamilton sees all the alien animals Superman rescued from the Preserver's ship, saying he could spend an entire career studying any one of them. Superman tells him that he usually doesn't bring anyone else up there, and that he only goes to feed the animals and steal a quiet moment for himself. Hamilton says if anyone deserves their own "Fortress of Solitude" it's Superman, who's not too crazy about that name.
Later, Jax-Ur and Mala take a leisurely walk through Metropolis, surveying their new territory, which Jax-Ur says they shall begin conquering just as soon as he is fully charged with yellow solar radiation, and thus Mala's equal. Mala can't help herself and begins to "play" with the humans, tossing cars about and such, causing a panic. At the Planet, Lois alerts Clark to the situation, telling him that Mala has returned and "brought a friend." Superman confronts his fellow Kryptonians, attempting to stop their rampage. He and Mala battle while Jax-Ur watches. Mala, a trained soldier, gains the upper hand and forces Superman to kneel before Jax-Ur. Jax-Ur says it would be a shame to kill one of the only other surviving Kryptonians, and that he is tempted to offer Superman a place is his new world order, if he wasn't so sure Superman would spit in his face. Superman confirms this, and uses his heat vision to melt a lamp post, which strikes Mala. Superman has no trouble taking out the weaker Jax-Ur before continuing with Mala. But when Mala inadvertently puts Lois in danger, Superman leaves to save her, giving Mala the chance to collect Jax-Ur and flee.
Back at STAR Labs, Professor Hamilton tests his new Phantom Zone Projector, which destroys its test subject. He tells Superman that the problem is that the machine needs a crystal that vibrates at the Phantom Zone's frequency, and that it simply doesn't exist on Earth, and without it they can't send anything into the Zone. Meanwhile, Jax-Ur and Mala attack the Daily Planet to kidnap Lois, knowing that she is the perfect bait to draw in Superman on their terms.
At the cabin, Mala is holding Lois captive. Superman arrives wearing his lead-lined suit and carrying a piece of Kryptonite that takes Mala down. Lois tells Superman that Jax-Ur is hiding in the forest, since he's not up to Superman's power level yet. Superman leaves the Kryptonite with Lois and goes to confront Jax-Ur, who appears suddenly with the Projector and sends Superman and the Kryptonite to the Phantom Zone. Jax-Ur orders Mala to let Lois live, as she's a reporter and can tell the world that Superman is no more, before destroying the Projector.
News reports show Jax-Ur and Mala attacking the United Nations Building, demanding to be given control over the planet. When the world leaders refuse, the pair begins to terrorize the entire world with their powers. Lois is with Professor Hamilton at STAR Labs, telling him that yes; Superman was in fact wearing his lead suit when Jax-Ur banished him. Hamilton says that they treated the suit with a radioactive element that they could use the current projector to detect and manages to draw Superman back into our world. The three return to Mala's cabin and Superman uses his super-vision to find the original Projector's tiny crystal.
The world leaders have given up and are about to surrender to the evil Kryptonians when Superman returns, challenging them to combat. They fight and chase Superman throughout the city, all the way to the rooftop of the Daily Planet building, where Lois and Hamilton jump out of hiding and use the new Projector to send Jax-Ur and Mala back into the Phantom Zone. Superman tells the pair that their parole has been revoked.
Back in the Arctic, Superman places the Projector beside the Brainiac Orb. He reflects on Hamilton's name for his refuge, "The Fortress of Solitude? It's not like I'm lonely up here" referring to the zoo filled alien animals. "But I am the only Kryptonian. And lately, I'm thinking that maybe it's better that way."