What is the Phantom Zone? Well, I'm glad you asked. On Krypton, criminals were once placed in suspended animation. But then, Jor-El discovered the Phantom Zone--a "twilight dimension" that exists outside of normal space/time. Put someone in the Zone and they become effectively immortal, but are no longer able to interact with our dimension. They can, though, observe us. So keep in mind the next time you're taking a shower, somebody in the Phantom Zone might be watching.
Jor-El invents a device that projects people in the Phantom Zone and this becomes the way Krypton deals with its violent criminals. Zod was sent there when he tried to conquer Krypton with an army of robots. Jax-Ur had tried world conquest at an earlier time, building a nuclear missile that blew up one of Krypton's inhabited moons when he test-fired it. (This, by the way, is why Kryptonians had abandoned space travel and were unprepared when the planet blew up.)
Superboy eventually found a Phantom Zone projector when he discovered a cache of Kryptonian weapons (shot to Earth by Jor-El years earlier). By the time he was an adult, he and a council of men from Kandor would form a Phantom Zone parole board to see which of the exiled criminals might have reformed.
Like many Silver Age Superman stories, this one jumps exuberantly from plot point to plot point. Superman is on the way to his Fortress of Solitude. But on the way there, he learns that the denizens of Atlantis are suffering from a plague.
This, by the way, isn't the Atlantis ruled by Aquaman. This Atlantis is inhabited by telepathic mer-people. Yes, the DC Universe has two separate and distinct undersea kingdoms. And why not? The bottoms of Earth's oceans take up an awful lot of square mileage, so there's plenty of room for two kingdoms. Though one of them really should have chosen another name. Apparently, undersea kingdom copyright laws are lax.
Superman can't find a cure for the plague, but during a meeting of the Phantom Zone parole board, the exiled mad scientist Jax-Ur claims to have reformed and know how to cure the plague. He's provisionally released for one day.
He and Superman then use a time capsule to travel back to pre-explosion Krypton, where Jax-Ur can find the element he needs to make the cure. They stop at the Jewel Mountains--formed eons earlier when now-extinct giant crystal birds came there to die. The Mountains are the skeletons of the birds.
The origin of the Jewel Mountains has absolutely nothing to do with the main plot. It's simply tossed in there because it's a cool idea. This is why I love the Silver Age.
Jax-Ur gets what he needs and cures the plague after returning to present-day Earth. But that's not the only thing he did while in the past. He also fiddled with the atomic structure of a chunk of the Jewel Mountains, so that it would become "Jewel Kryptonite" when the planet exploded. He's also calculated that this particular chunk of the mountain will be blown towards Earth.
Jax-Ur is sent back to the Phantom Zone until the next parole hearing, but that's just fine with him. Because jewel kryptonite allows him and the other Phantom Zone criminals are now able to focus their mental energies and cause explosions on Earth. They start blowing up gas and oil storage tanks whenever Superman is nearby, causing him to think that jewel kryptonite has made him a danger to those around him.
Did I say the story jumps from plot point to plot point with exuberance? It actually jumps with wild abandon. But it has fun while doing so and--like so many other Weisinger-era stories--it manages to follow its own internal logic. This is something I know I'm making ad nauseum when I talk about these stories, but it's important. It's what made the stories work as stories--they make sense in a way that we readers can understand. Despite the innate silliness of it all, Superman's universe and the stories being told about that universe had a definite structure.
Oh, well, it's still a good story. The Phantom Zone criminals were used on occasion throughout the Silver Age--often with quite clever plot devices being employed to get them into the story. According to the DC Wiki, Jax-Ur had 30 pre-Crisis appearances, while General Zod had 39. Eventually, Zod would grow more prominant and Jax-Ur would fade into comic book obscurity. But Jax-Ur managed to get in a fairly respectable career as a super-villain nonetheless.