The Superboy that would survive the original Crisis hailed from Earth-X which was a copy of our reality in which superheroes only appeared in comic books, with the exception of him. He was introduced just a couple of years prior to the Crisis, but proved instrumental in defeating the Anti-Monitor.
While in the paradise dimension Superboy is becoming increasingly frustrated with how dark and dangerous the DCU has become over the preceding twenty-years. With Alexander Luthor Jr. whispering in his ear, feeding his anger, and manipulating him into trying to break out of the paradise dimension they had been sequestered in. As Superboy raged savagely against the walls of their pocket dimension he caused all of the wired and odd changes in continuity, such as the return of Jason Todd.
Once on Earth, Luthor continues to manipulate a confused Superboy. Losing his anger in battle against a number of heroes including members of the various incarnations of the Teen Titans during the inter-Crisis period. At the peak of battle, Superboy-Prime kills former Titan Pantha (first appearance New Titans #73 (February 1991), which sets him down the road to becoming one of the most fearsome and powerful villains in the DCU; donning the remnants of the Anti-Monitor’s armor.
In his last heroic act the Superman of Earth-2 helped the heroes of Earth-1 defeat Superboy-Prime and Alexander Luthor Jr.’s machinations. Superboy-Prime is imprisoned on Oa under the charge of the newly reformed Green Lantern Corps, but not for long …