Jon Kent in the New 52 was kidnapped by Harvest and trained to become a Meta killer, however the yellow sun that gave him his powers was also killing him. Jon passed out so Harvest was forced to create a clone, Superboy, to not only wipe out all the Metahumans but also stabilize Jon.
Jon is first encountered by the Teen Titans after they were thrown into the future by Johnny Quick, where they find the superhuman population decimated by the son of Superman: Jon Kent, whom Kon-El was cloned from. After a confrontation with the Justice League of this era, lead by a grown up Beast Boy, Conner is attacked by Jon while alone.
The confrontation ends with Con grievously wounding Jon, but is then pulled back into the timestream. The League finds Jon unconscious, and in hopes of preventing their present, dresses Jon in a costume like Con's and sends him with the Titans who are unaware of the switch.
As Jon wakes up, he pretends to be Conner while plotting his next move, realizing that he could end up back in time and prevent himself from becoming the monster he is by preemptively killing off all metahumans and finding a cure for himself. So far however his plans have hit a snag, of sorts, as Raven has seen through the deception but is currently permitting and subtly aiding his continued venture, as it furthers her own goals for the time being.
Major Story Arcs
Whatever Happened To The Man of Tomorrow?
After Superman removed his powers using gold kryptonite, he settled down and lived a normal life under the alias Jordan Elliot. He and Lois had a son named Jonathan.
Son of Superman
15 year old Jonathan "Jon" Kent never knew his father, as he disappeared before Jon was born. And his mother, Lois Lane, never told him that his father was Clark Kent (better known as Superman). However the truth came out when a solar storm's radiation triggered Kryptonian powers in Jon. Jon was approached by a terrorist group funded by Lana Lang, to find Superman, who she believed was being held prisoner in a secret lab. Jon, now in his newly designed costume and identity of Superboy, is able to successfully free Superman. Superman and Lois have a tearful reunion, but Jon is not content to suddenly have his father back in his life after 15 years. But when it is revealed that Lex Luthor, the new head of the Justice League of America, was responsible for Superman's capture, Superboy teams up with his father, along with Batman and Wonder Woman to stop him. However Luthor had decoded Superman's DNA and was able to give himself Kryptonian powers. After a prolonged battle, Superman and Superboy were able to defeat Lex. Superman, Jon, and Lois finally come together as a family, and Jon is given his father's original costume to wear as Superboy. Superman decides to temporarily retire from being a superhero to focus on being Clark Kent again, and being a good husband and father. This leaves Jon to be the first of a new generation of heroes.
Powers & Abilities
Jon is a Kryptonian/human hybrid and has powers of superhuman strength, superhuman speed, Super Sight, flight, and invulnerability. As a hybrid however he also has abilities neither parent race possesses, such as telekinesis.