Kal-El was born as the son of Lara and Jor-El of the planet Krypton in the Pre-Crisis universe designated as Earth-Prime. When Kal-El was still a toddler, his scientist father made a grave discovery. Jor-El learned that a massive solar flare from Krypton's red sun threatened to engulf their home world, ultimately destroying it. Jor-El brought his concerns to the Kryptonian Science Council, but rather than offer solutions, they politicized the pending travesty and locked themselves in committee.
In the meantime, Jor-El labored to find a way to save the people of Krypton. Working alongside his scientist wife, Lara, they developed a technology which would enable them to teleport samples of living tissue (weighing less than fifty pounds) across intergalactic distances. He presented his transportation device to the science council, but it was too late. Krypton was already beginning to suffer from the effects of the intense solar radiation. As Krypton shook in its death-throes, Jor-El placed his son inside of the teleportation device and transported him across the universe.
Kal-El rematerialized on the planet Earth. In a New England seacoast town, Jerry and Naomi Kent were hiking through the forests when they discovered the abandoned toddler. They decided to adopt him and raise him as their own. Naomi chose to name him Clark, despite the fact that Clark Kent was the name of a popular comic book hero known as Superman.
Unlike his namesake however, Clark Kent grew up without the benefit of super-powers. His classmates at school would tease him and refer to him as Superboy. However, Clark took the ribbing in stride and soon cultivated a small circle of friends.
As Clark grew older, he became romantically involved with a fellow student named Laurie Lemmon. One evening, Clark, Laurie and several other friends decided to attend a costumed beach party. Being of good humor, Clark donned a Superboy costume similar to that worn by the fictional comic book hero. They drove down to Hampton Beach and sat by the ocean waiting to catch sight of Halley�s Comet.
Suddenly, a tremendous tidal wave rose up on the beachhead threatening to flood the small hamlet. At that same moment, a cosmic vortex opened up above them discharging the Earth-One super-hero known as Superman. At that critical moment, a bizarre transformation took hold of Clark. The physical characteristics of his Kryptonian heritage manifested for the first time and he discovered that he was gifted with flight and super-strength.
Superman quickly introduced himself to his younger alternate Earth counterpart, but there was little time for pleasantries. Superman gave Superboy a crash course in the use of his powers and together, they were able to divert the course of the deadly tidal wave.
With the immediate disaster abated, the newly crowned Superboy aided Superman in returning him to his proper world. He followed Superman through the cosmic vortex to Earth-One. Little did Superboy realize that he would never again see his adopted world.
Crisis on Infinite Earths
The Multiversal catastrophe known as the Crisis on Infinite Earths began as a deadly wave of anti-matter consumed parallel dimensions. Superboy aided heroes from hundreds of different worlds, but none of them were able to save the Earth of his home dimension from destruction.
The Crisis finally culminated with the destruction of the Multiverse. In its place existed a solitary static universe with only one version of the planet Earth. Superboy-Prime remained as the sole survivor of not only his birth world, but his adopted world as well. He united with an aging version of Superman from the late Earth-Two as well as his wife, Lois Lane-Kent. Along with Alexander Luthor, Jr. of Earth-Three, they traveled into the Antimatter Universe and forged a quiet, peaceful existence for themselves in a paradise realm.
Over time, as the four of them watched the history of the New Earth reality unfold, Superboy-Prime became frustrated and angry, homesick and wishing to return to the life he had. He consoled himself by watching images of his ninth birthday and grew horrified every time it would focus back on the Crisis. Alexander would notice that and decided to manipulate him to his needs. On two separate occasions, Superboy-Prime's anger got the best of him and he shattered the wall with his fists, the punch altering reality as it did. Upon deciding to join Alexander in his quest to bring about the perfect Earth, Alex empowered him with his Anti-Matter powers using it to break free. He was spotted by Blue Beetle, but Prime ignored him. In quick succession, Superboy-Prime obtained the Eclipso diamond to be obtained by Jean Loring, altered the location of Thanagar, initiating the Rann-Thanagar War and attacking and capturing J'onn J'onzz, destroying the Watchtower.
When Alexander convinced Kal-L to leave their paradise reality, Prime was already with them, no one the wiser over what he had done. Soon after being freed, Prime was there to greet Power Girl after she was reunited with her cousin. However, when she discovered Alex's tower, Prime struck her down to be used for it. He then flew to Smallville, Kansas where he encountered the Superboy of this reality. He chastised the clone Superboy and accused him of being unworthy of the title of Superboy. The two fought one another and their epic battle raged across the state, eventually culminating in Keystone City. Members of the Doom Patrol, the Justice Society, and the Teen Titans arrived to lend a hand, but the power-mad Superboy-Prime thwarted even their efforts. He brutally attacked the heroes, killing several including Pantha, Bushido and Wildebeest. Jay Garrick, Wally West, and Bart Allen, grabbed Superboy-Prime and used their combined super-speed to propel him into the kinetic dimension known as the Speed Force.
However, Superboy-Prime escaped from his imprisonment and built a battle-suit based on the Anti-Monitor's armor that constantly supplied his body with yellow sunlight. Superboy-Prime arrived at Alexander Luthor's tower to battle with Nightwing, Superboy, and Wonder Girl (Cassie Sandsmark). The heroes succeeded in releasing the metahumans powering the machine. After a brief fight, Conner grabbed Superboy-Prime and flew into the tower destroying it. However, Superboy-Prime would be unfazed by the attack, escaping as Conner was killed by the rubble.
Superboy-Prime then was seen at the Battle of Metropolis, killing both heroes and villains with ease. He continued his killing spree until he was met with resistance by Bart Allen in his grandfather's uniform. He was pulverized by Bart, but then left Earth to destroy Oa in an attempt to cause another Big Bang and reform the current universe hopefully closer to his original Earth-Prime reality. On the way to ignite this universal rebirth, Superboy-Prime killed 32 Green Lanterns. Then, while battling the Green Lantern Corps, Kal-L and Kal-El forced Superboy-Prime through Krypton's red sun to depower the vastly overpowered youth to levels where the elder Supermen could handle him directly. The three crash-landed on the Green Lantern planet Mogo, where they continued to fight. Kal-L's power levels were intact, but was still no match for even the power fading levels of Superboy-Prime, who was able to literally beat Kal-L to death with his bare fists and was able to fight against the New Earth adult Kal-El, whose own superpower levels had completely faded. But the time and effort Superboy-Prime used to attack Kal-L (whose strength and endurance was still superhuman) was enough to completely drain off Superboy-Prime's own power level to where the fully adult New Earth Superman was able to beat the still only teenage Superboy-Prime.
Superboy-Prime was then taken into the custody of the Green Lantern Corps. Too powerful to be placed in a regular Sciencell on Oa, the Guardians of the Universe imprisoned him inside a Sciencell near what is alternately described as a red sun or a Red Sun-Eater, constantly being guarded by fifty Green Lanterns. Members of the Corps were often assigned to "Prime Duty" as punishment. While in prison, Superboy-Prime carved a bloody "S" on his chest using his fingernail, saying that he had always found a way out (referring, presumably, to his escape from the Speed Force and his future prison).
Sinestro Corps War
Superboy-Prime was freed, along with the Cyborg Superman, by a strike force of Sinestro Corps members who turned the red sun to yellow, presumably thereby restoring his powers. Superboy-Prime was brought to Qward, where he was made into a herald of the Anti-Monitor, along with Cyborg Superman, Sinestro and the Parallax-possessed Kyle Rayner. 
Now calling himself Superman-Prime, Prime joined in the battle to attack most of the major heroes of Earth as part of the strike force of the Sinestro Corps. And again, due to the massive power difference between himself and the others, Prime was able to cut a path of destruction throughout the known universe, once again successfully defeating Kal-El of New Earth, but this time with Power Girl and Supergirl all at the same time with them charged up as well, ending the debate of who was the most powerful of the Supermen as well as many other high powered heroes in his role as the herald of the Anti-Monitor.
However, Prime showed that his main goals are to gain his revenge on the Anti-Monitor (who Superboy-Prime had accidentally revived during Infinite Crisis) and somehow recover his lost universe, or at least the recognition as the so-called "real" Superman over weaker incarnations such as the adult Kal-El of New Earth.
Towards the end of the Sinestro Corps War, Prime was confronted by the Guardians of the Universe, who introduced the new Ion, the Daxamite Sodam Yat. Prime and Sodam Yat battle each other in a brutal and fierce fight. It is clear that Prime is clearly more powerful than Yat, though Yat refuses to yield in any way. When the battle is taken inside a nuclear power plant (with its walls lined with lead), Ion is obviously weakened by lead poisoning to the point that he can not even really fight back against Prime. Prime spears Ion with several lead rods, then beats him unconscious and leaves Yat for dead until the Guardians prevent him from actually killing Yat.
Later on, during the final battle between the Green Lantern Corps and the Sinestro Corps, the Anti-Monitor is severely injured when the Green Lanterns throw Warworld at him and the Cyborg Superman like a grenade. Prime takes this opportunity to turn on him and throws the Anti-Monitor into deep space. Prime is then attacked by both Corps and kills several members from both sides. Before any more lives can be lost, one of the Guardians uses himself as a living bomb and detonates himself to kill Prime. The explosion does not kill Prime, but merely transports him into the Multiverse. An unexpected result of the transport was that Prime's atoms are infused with a large portion of the Guardian's own energies that the Guardian thought would destroy Prime. The infusion of the Guardian's energy as part of his energy absorption and processing ability restructures his body to now appear as a fully adult man rather than his actual age of only 19.
During Countdown, the now adult-looking Superman-Prime has started a murderous rampage against all of his other dimensional counterparts and their supporters while searching for Earth-Prime. Superman-Prime was shown killing the Superman of the Earth-15 dimension and his wife and unborn child. After killing that world's Justice League, Superman-Prime destroys Earth-15. Returning to his new base of operations, the Source Wall, Superman-Prime is shown torturing Mr. Mxyzptlk and Annataz Arataz of Earth-3 to recreate Earth-Prime using his super-science/magic abilities or at least show him its location in the Multiverse. During his torture, Mxyzptlk reveals to Superman-Prime that his aging to adulthood was from him absorbing the cosmic Oan powers of the Guardian that blew himself up to kill him during the Sinestro Corps War. He also tells Superman-Prime that the cosmic energies will wear off very soon, and then he will turn back into a boy. After he escapes, Prime is angered and gives up on the use of magic to achieve his goals.
After finding out about the so-called perfect universe which he thinks is his original source universe, Superman-Prime heads off to the Monitor's satellite headquarters, threatening the brutal Earth-8 Monitor Solomon to help him find this recreated Earth-Prime. Superman-Prime demands to know where this "perfect universe" is. Seeking to manipulate the infinite powered Superman-Prime to defeat the Monitors' forces against those of Monarch for the Monitors, Solomon sends Superman-Prime to Earth-51.
As Solomon predetermined, the successfully manipulated Superman-Prime flies to the battlefield to challenge Monarch, in order to keep him from destroying Earth-51. Superman-Prime goes into a rage and attacks Monarch, with his cosmic powers seemingly beginning to dissipate. Prime then tears off the chestplate of Monarch's containment armor. The energies inside Monarch's armor are released, resulting in an explosion of quantum energy so massive, it destroys the entire contents of the Earth-51 universe.
Final Crisis: Legion of Three Worlds
Prime had been lost in the timestream following his final encounter with Monarch. The Time Trapper brought Superboy-Prime to the 31st century in his never ending scheme to destroy the Legion of Super-Heroes. He crashes into the 31st Century a little bit outside of Smallville. His stolen Oan energy at this point had faded, reverting him to his actual young age, as well as returning his power to their previous levels, which was what Mr. Mxyzptlk had foretold.
Upon arriving, he is encountered by a old farming couple, who thinks he's Superboy, which makes him extremely mad. He considers himself a man, not a boy, and kills the couple. When he flies to Smallville, he comes upon the Superman Museum, further fomenting his fury at how beloved Superman is in the future. He then becomes even more enraged when he sees the hall of villains, only to find out that he is not even considered a villain of Superman's, but no more then a nuisance and his statue is kept in storage. Furthermore, history retells that he was defeated by Conner Kent and Sodam Yat, totally contrary to what really happened. He proceeds to wreck the entire museum and kill whatever security or police officers he comes across. The Museum tour guide (a holographic recreation of Jimmy Olsen) then tells Superboy-Prime of the Legion of Super-Villains.
When Superboy-Prime learned that the Legion of Super-Villains followed a code of evil, inspired by a dark being whose "name was never spoken," he got the idea to be the greatest villain Superman had ever faced. Superboy-Prime then went to the prison planet Takron-Galtos and freed the imprisoned Lightning Lord, Saturn Queen, and Cosmic King. When they see Superboy-Prime, they immediately know him and hail him as the inspiration of the LSV's evil code, making him the dark being in question. He then burns an S shield into the planet, that can be seen from space.
When the Legion of Super-Heroes learns of the prison break, they decide they need to bring Superman from the 21st Century. Superman and Brainiac 5 decide to bring in two other versions of the Legion to combat the Legion of Super-Villains. Superman believes the only way to stop the carnage is to try to redeem Superboy-Prime.
Superboy-Prime later makes his way to Sorcerer's World where he recruits Mordru to his Legion and kills the "last" active Green Lantern, Rond Vidar. Legion members Mon-El and Shadow Lass follow Vidar's ring back to Oa and find that Sodam Yat is still alive and had been monitoring the last Green Lanterns. They convinced him to battle Superboy-Prime once again. With Yat, Superman, and the Legions of two other dimensions as reinforcements, the Legion was able to turn around the battle with the combine forces of all their major villains in Metropolis.
Superboy-Prime burned a hole through Superman's hand and broke through Yat's ring construct just in time to be informed that there was something happening at Legion headquarters. At the headquarters, three Brainiac 5s, Lightning Lads, Lightning Lasses (one of whom is actually Light Lass), and XS, using a combination of living lightning and a Cosmic Treadmill, bring the young version of Bart Allen out of the Speed Force. Superboy-Prime is seemingly distraught at the thought of Bart's return, since he is the only person that was able to defeat him twice.
Not long after fighting Kid Flash, Element Lad arrives and and turns the surrounding debris into Kryptonite, which actually causes harm to Superboy-Prime, but he then kills Element Lad by throwing a piece of Kryptonite right through him. Cosmic King then turns the Kryptonite in Superboy-Prime's body into yellow sunlight. When the LSH head to the North Pole to regroup, Superboy-Prime and the LSV follow them to the Fortress of Solitude. He attacks the three Brainiac 5's and cuts off Polar Boy's ice hand. Wildfire then uses his powers to fuel a Kryptonian regeneration chrysalis inside the Fortress. From the chrysalis emerges a resurrected Conner Kent, a.k.a. Superboy, his corpse having been placed in the chrysalis by the LSH when they time-traveled to the 21st century as part of Brainiac 5's plan to recall Superboy-Prime's greatest enemies to the future to stop him. Superboy and Superboy-Prime clash with the rest of the Legion joining in.
During the latest battle with the Time Trapper, Superman pulled off the Time Trapper's hood to reveal an aged Superboy-Prime as the Time Trapper's real identity.
As the Legion continue their battles, the Time Trapper reveals that he knows the outcome of the battle, claiming that the Legion loses on this day. But, as the battle rages, Conner inflicts a wound on Superboy-Prime's body, burning a scar across his S-Shield-scarred chest and inflicting it upon the Time Trapper. Realizing that time, and thus his own body, is fluid, Superman, Saturn Girl, Cosmic Boy and Lightning Lad defeat the Time Trapper and drag him to the battlefield where the two Primes meet. The Time Trapper attempts to recruit Prime in destroying the Legion, but Prime, whose arrogance means that he is unable to accept that he will become someone like the Time Trapper, attacks the being, causing a time paradox that apparently wipes both of them from existence.
Instead, Superboy-Prime is flung back to a recreated version of Earth-Prime and reunited with his family and girlfriend. Instead of being greeted with open arms, Laurie runs away, horrified at Superboy-Prime and his father confronts him over what he did. Prime learns that his parents and everyone else had read what he did in Infinite Crisis, the Sinestro Corps War, Countdown and Legion of 3 Worlds. His adoptive parents, now afraid of him, allow Superboy-Prime to remain at their home, fearful of what he may do.
Superboy-Prime is last shown with his eyes powering up in his parents basement, trolling the various DC Comics message boards, trying to prove his greatness and vowing that he will find someway to return to his former power and threat levels once again as he has shown he is committed to being the most powerful villain ever.
In Adventure Comics (vol. 2) #4, Superboy-Prime is seen again, still reading comics in his basement, trying to keep up with everything in the other worlds. When he learns of his fate at the end of this issue, he panics and demands his parents take him to the comic store, the Legion watching as he does. As they get there, Naomi reveals that she's afraid of him, but he brushes it off. In the comic store, he demands to know where Adventure Comics (vol. 2) #5 is, but the comic store cashier tells him that issue #4 just came out. He then tells him to look up possible spoilers on the Internet. As he does, Alexander Luthor appears, now a Black Lantern, killing the cashier and a customer. He confronts Superboy-Prime, wanting his heart. Superboy-Prime stops him briefly, knowing that this isn't the real Alexander Luthor. Luthor, in turn, grants Prime back his armor, returning him back to Superboy-Prime.
Superboy-Prime goes on the attack, but Alexander continues to taunt Prime, telling him that he's nothing more than a cosmic inside joke. Prime is then weakened and struck down by other forces. Looking up, Prime discovers Black Lantern versions of those he killed, including Element Lad, Charaxas and Bushido, with Alexander telling Prime that he will die in the next issue.
The next issue, Superboy-Prime is seen having taken the battle from his hometown to Manhattan, where he crashes through the DC Comics headquarters, where he decides that, if he's going to die, he's taking the writers and plotters who made his life that way. Before he can, though, Black Lantern Alexander Luthor arrives and pulls Prime away, taking him back to his room. There, Alex taunts him over losing Laurie as the other Black Lanterns beat him down and tear away his armor. Realizing he can't win, he catches a Black Lantern Ring and puts it on, the ring commanding him to die.
As he becomes Black Lantern Superboy-Prime (realizing Alex's cryptic statement at the end of the final issue), the ring cycles through the Emotional Spectrum: willpower due to his deluded demand for respect, compassion for regretting what he did to Laurie, avarice for wanting everyone to love him, fear of those he wants admired, and stopping at rage for hating himself for what had become, transforming into Red Lantern Superboy-Prime. He goes into the offensive, attacking Alex over his attacks. At the very end, the ring asks him who does he love. He calls out that he loves Laurie, transforming him into the Star Sapphire Superboy-Prime with the last of his strength. As he passes out, the Black Lantern Ring shatters, unleashing the white light and eradicating the Black Lanterns.
In the end, he admits that he hates what he has become and all he wants now is just his happy ending. As if someone was listening, Laurie appears, her arm in a sling (meaning that the horrible thing Superboy-Prime did to her lead to her having broken her arm). She tells him that they (possibly the writers) have heard his pleas and sent her to tell him that they're going to start leaving him alone. Unbeknown to him, she's also wearing a Black Lantern Ring, but this one sparkling with hope, the last of the emotions that Prime wasn't asked about.