Kon-EL is the half-human half-Kyrptonian clone creation of the mysterious organization N.O.W.H.E.R.E., which seeks to control the new generation of metahumans. His main power is telekinesis, which he uses to simulate full Kryptonian abilities, and he is sent out on missions by the organization. He comes to the attention of the newly formed Teen Titans, and battles with them, during which he realizes he is merely the "living weapon" of N.O.W.H.E.R.E., and spends time by himself. During this time, he encounters Supergirl, who explains to him his Kryptonian heritage. Sharing her people's prejudice and hatred of clones, Supergirl names Superboy "Kon-El," a Kryptonian word that means "abomination". He also learns he is N.O.W.H.E.R.E.'s second Superman clone, but cannot extract more information about this from N.O.W.H.E.R.E. mercenary Rose Wilson, who defeats him in combat. The Teen Titans later stage several rescue attempts on Superboy, and eventually recruit him to the team.
He is attacked by a time traveling Kryptonian named H'El for being a clone, after which H'El delivers his body to Supergirl and Superman for execution. As clones were generally hated by Kryptonians, H'El believes this act will prove his loyalty to Krypton, but it instead triggers conflict between him and Superman, who doesn't wish to kill Kon-El. During the fight against H'El, Superboy and Superman come to know each other better and develop a feeling of friendship and understanding. Kon-El is surprised by Superman's heroism and is touched by it.
The evil speedster Johnny Quick throws the Teen Titans forward in time. After he is separated from the Titans, Kon-El encounters Jon Lane Kent, the villainous future son of Superman and Lois Lane. Kon-El is actually a clone of Jon Lane Kent, created by Harvest (founder of N.O.W.H.E.R.E.) so that a cure could be found for Jon's illness. During their battle, Jon Lane Kent is seriously injured but then Kon-El falls through a portal and is transported to Krypton's Argo City in the past, days prior to planet's destruction. Kon-El uses the last of his powers to lift Argo City off of the dying Krypton, saving it so that a young Supergirl can arrive on Earth just as history records. He then dies with the planet, accepting himself as more than a "living weapon".
The unconscious and injured Jon Lane Kent is recovered by the Beast Boy and Rose Wilson of that future time period. They know that this Superboy is actually Jon Lane Kent but, for their own purposes, hide this fact and dress him in Kon-El's costume. The Teen Titans then arrive and assume that this is the Superboy they know (they were unaware of Jon Lane Kent's existence or that Kon-El encountered a villain with identical appearance and powers). The Teen Titans then take Jon Lane Kent back to the modern day era and he pretends to be their version of Superboy. Although Superman and Supergirl know that Kon-El is dead, they have not told the Titans. No one on the team is aware yet that Kon-El is dead and that they have an impostor in their midst who intends to kill all of Earth's meta-humans.