Though "Man Who Destroyed Krypton" is executed by Otto Binder and Al Plastino, two regulars in editor Mort Weisinger's stable, the story's also an early example of a comic-book "retcon." Usually in the Weisinger-verse, newer stories rewrote older ones with no concern as to what had been established before. However, this time there seems to be a marked attempt to play to fannish ideas of "continuity" by proposing a new paradigm-- though it was one that largely renounced by both fans and later professionals.
Oddly, the tale begins with Superman learning of an extraterrestrial menace from mundane law enforcement authorities. Through their sources, the top cops have established that an alien operative, Black Zero, plots to destroy the Earth. Superman locates the alien, who has a bit of news for the Kryptonian. Years ago, Zero was sent to destroy Krypton because his bosses, a planetary combine called "the Pirate Empire," feared the planet's culture could prove a threat to their conquering aims. Before he even tried to eradicate the world, though, Zero encountered the warnings of Jor-El, to the effect that the world was already on the brink of destruction. Zero checked things out, and found that Jor-El was wrong, but that the nuclear reaction inside the planet could be re-started. Thus, Black Zero, rather than cruel fate, was responsible for billions of dead Kryptonians.
Thus, Superman's mission becomes twofold: he must both save the Earth and capture the destroyer of Krypton. (Preumably Zero has destroyed other worlds for the Empire as well, though somehow these other worlds are never mentioned.) Zero eludes the Man of Steel, but the hero receives help from one of the Phantom Zone prisoners: Jax-Ur, who was in Silver Age SUPERMAN stories was usually framed as the brains behind the other Kryptonian criminals. Jax-Ur and the other Zone crooks are genuinely desirous of vengeance for their homeworld, and they persuade Superman to release Jax-Ur alone, after he swears a criminal's oath not to double-cross the hero.
Naturally, Superman succeeds in thwarting Zero's plans for Earth, and Jax-Ur gets the chance to take the vengeance that Superman won't take: turning Black Zero into a stone statue and then smashing it to bits.
The story's most interesting myth-moment is not so much the rewriting of Jor-El's doomsaying-- which, as I said, most fans did not like and which most pros ignored-- but the fact that the theme seems to be "set a genocidal madman to catch a genocidal madman." For Jax-Ur is sent to the Phantom Zone for a sort of "accidental genocide," in that he's testing a missile and unintentionally destroys a Kryptonian moon inhabited by 500 people. Binder's story does not reflect on Jax-Ur's past history, but since Binder created the story in which Jax-Ur first appeared, it's at least feasible that he remembered that bit of continuity-trivia when he chose Jax-Ur to be Superman's ally.