Sinister Scientists Secluded in Shadowy Subspace

The Phantom Zone... the repository of the most vile criminals from the planet Krypton-One once Jor-El had discovered it... within only a few years was abandoned as to inhumane to imprison its illegal occupants. However, shortly thereafter that world exploded, and it would be years later when Jor-El's son Kal-El received the Phantom Zone Projector when Superboy would first encounter this now superpowered foes. Yes, they gained superhuman abilities like the Boy of Steel under Earth-One's yellow sun, and so individually and collectively, these criminals would face off versus their prisoners's son repeatedly through the years. And each universe has a similar twilight dimension adjacent to or, as evidenced by the appearance of Jur-Ll of Krypton-Three who used his Zone to travel to Earth-One's city of Kandor.

Since the Zone was a manifestation of an alien entity of its universe known as Aethyr, there was no corresponding entity or pocket dimension like the Zone through which Jor-L of Krypton-Two could transport his planet's criminals to... and in fact there is no record of any such infamous individuals having existed there. However, as often happens between these two universes, counterparts sometimes come from different places in each realm.

This was similar to the precedent set by Thanagar-One's Hawkman and Earth-Two's Hawkman, neither a native of his doppleganger's home world. Since Jor-L did not have opportunity to discover his own Phantom Zone, it was left to various scientists of Earth-Two to find the means to pierce the dimensional barrier into this new plane of existence. However, those men of Earth-Two who did so utilized access to it not to imprison felons but to bribe the innocent and empower their crooked cronies. Vandal Savage inadvertently became a transdimesional phantom in this realm like his cosmic twin Kru-El, when he tried to expose himself a second me time to a flaming meteorite that originally gave him immortality… hoping to gain new life from it. Then there was Professor Hunt aka Maligno of Earth-Two, counterpart to Doctor Xa-Du who with his wife used sinister science to torment Superboy and, years later, Superman.

Zoners manipulated the Flash three times, first when Luther Jarvis mentally controlled the Scarlet Speedster, sending him against Earth-Two's Spectre. After this, a quartet of crooked Kryptonians led by Jarvis’ counterpart Professor Va-Kox orchestrated a race between Flash and Earth-One's Superman, in order to open a path out of the Zone. And later Va-Kox’s allies mentally manipulated Flash against Superman shortly before the Fastest Man Alive’s death during the Crisis on Infinite Earths.

And, in fact, the Zoner's counterparts originated on Earth-Two, and as such encountered either that world's Superman or his allies in the Justice Society. The scientist that pierced the barrier into what was known as the Fourth Dimension, was Anton Unreal aka Uriah, who like his cosmic twin Quex-Ul aka Charlie Kweeskill of Krypton-One knew secrets of these shadowy realms. While those in the Zone could become phantoms, so too were the so-called “Spirit-Masters” who were other individuals whom Unreal exiled to this realm prior to his imprisonment of Steve Trevor. This led to his girlfriend Wonder Woman intervening to save him. Several of these Masters had been around a few years earlier when they battled the heroine’s Justice Society teammate the Spectre. While the fearsome phantoms that plagued Earth-Two actually originated from that planet rather than their universe's Krypton like their dopplegangers, they had powers comparable to the Kryptonians within their twilight dimensional analogue to the Zone.

Foremost among these was the megalomaniac Zor, the counterpart of General Zod himself. Although he was originally a prominent military leader of Krypton-One, Zod sought to usurp control of the planet's government then ruled by the Science Counsel, which he bitterly opposed. To that end, Zod crested an army of imperfect duplicate of himself to provide him the "manpower" to enact his scheme. Failing at this, his banishment into the Zone began an adversarial relationship between he and the house of El of whom Jor-El was his prime opponent. As the scientist perished along with most Kryptonians, he sought victory over his foes’ son, Kal-El. However, Kal as Superman repeatedly outmaneuvered the military strategist, despite Zod's near perpetual command over his fellow Zone prisoners. Zor was himself a disenfranchised member of a mysterious organization that decided to use his superhuman powers for conquest. This led him towards several battles versus his arch enemy the Spectre, and eventually appeared as a globe-being to battle the Justice Society, much as Zod had employed globe brains from space versus the Legion of Super-Heroes. Zor was kept imprisoned for indeterminate periods of time by his adversary.

Then there was the Kryptonian scientist Kru-El, cousin of Jor-El who like his counterpart Vandal Savage was a procurer of illegal weaponry with a thirst for power. Two other malevolent masterminds in  Gaz-Or and  Bandar were among the worst of their lot, given the crimes they orchestrated. There were others such as Thul-Kar and Kalthoon who styled themselves as prophets, although they were actually master manipulators. Then there were the more common criminals, such as Gra-Mo and Ace Chance. who along with countless others were occupants of these other realms adjacent to the twin Earths sought to plunder from others. 

Even some unspecified occupants of the Spectral Zone or Fourth Dimension enlisted by Kalthoon who like various unidentified prisoners of the Phantom Zone were recruited into Zod's phantom army.