Superboy: Origins of Kon-El

Summary: Sequel to my Superman Returns story. Lex escapes from jail, obtains a sample of Superman's DNA and uses it to create a clone as part of his final revenge. During this Lex comes to a revelation regarding his one time best friend. One Clark Kent.

Disclaimer: I don't own any of the characters I use in this story.

Author's Note: In my epilogue to my Superman Returns story I mentioned Clark's clone Kon-El and I always wanted to go back and elaborate on how he came into being so I did. Here is the story of his creation and how he ended up making the choice on which side he would end up on. I'll add a little reminder that I mashed a little bit of Smallville into my story so that like on the show Lex and Clark were once friends.

Chapter 1: Birth

He was Lex's greatest creation. From a sample of Superman's blood Lex had succeeded where teams of scientists had failed. He had created a successful clone of Superman. Well if Lex was to be entirely honest what he had created wasn't a clone so much as an offspring. Kryptonian DNA was complex and every attempt to get it to replicate properly had failed. Even he had failed the first few times. The DNA would become unstable and break down until Lex realised that he needed to add a stabilising element. That stabilising element was human DNA and not just any human DNA. Lex decided to use the best. His.

Lex places his hand on the maturation tube his creation slept in. From the efforts and research of others Lex had also managed to come up with a method to accelerate the ageing process so that in a matter of weeks the male offspring was now a teenager. A familiar looking teenager. The physical attributes were all Superman's as Lex knew they would be. He had used his own DNA simply to fill in the gaps in the genetic sequence. Too much and the boy would be too human and not of any use since he risked watering down Superman's abilities too much if he did that.

However it is not the resemblance to Superman that intrigues him right now. It is the resemblance to his dear old friend Clark Kent that intrigues him. The clone looks exactly like Clark did when Lex first met him back in Smallville. Lex had always suspected that there was more to Clark Kent than met the eye. Now he knows what secret it was that Clark was keeping. It all makes sense now. The meteor shower of kryptonite that hit Smallville. It had been dragged along in the wake of Superman's ship upon its landing on Earth when he was an infant. The Kents must have found the ship and taken the infant Clark in. Lex knew that they had adopted Clark when he was about 3 years old. And of course that explains why Clark vanished shortly after he turned 18. He had been called to the Fortress where he learned who he was. Lex had been dealing with pieces of the puzzle for years and now it all finally fitted together.

He would wake the clone up soon. In a day or two. Lex supposes you could call that day the clone's birthday. He was going to call it Kon-El. An anagram of clone if you replace the C with a K. Lex thought it fitting. The clone was now part of his plan to gain his final revenge on Superman...on Clark. Now Lex had this knowledge it actually made it easier. He would have Clark watched. Figure out his routine. Lure him into a trap Lex was preparing and leave him alive just long enough to tell him what he had figured out. Have a final tête-a-tête as it was. Then Lex would kill him. Lex's final revenge. After Clark had taken so much of his life away and now Lex would permanently take Clark's away. The Justice League would no doubt try to interfere but they would be dealt with too. Divide and conquer was an old but still very effective strategy if employed correctly. The League had many enemies that could aid Lex in this endeavour.

"You know I thought I was an affront to nature but that thing there has me beat," Lex's ally says with morbid humour. The ally that had busted him out of prison and had gotten the blood sample from Superman because few others were actually capable of hurting the Kryptonian boy scout let alone do enough damage to make Superman bleed.

Lex eyes his ally at the threshold of the room. "I told you not to enter here. Your kryptonite heart risks destroying all my work," he reminds his ally.

Metallo would roll his eyes if he still had any and not these robotic sensors. He was perfectly well aware of what his heart would do to Lex's little lab rat. He was not a mindless robot. He had once been a man named John Corben until one day he was in a car accident and the next thing he knows some whacked out scientist had transferred his brain into a robot body powered by kryptonite. Metallo killed him for that. Killed him in memory of John Corben who is dead. John Corben had been a man. Metallo was a freak. A human brain in a robot body that can't feel anything. Not touch nor taste nor smell. Metallo lived to wreak vengeance in John Corben's memory. And he did until Superman stopped him. Despite his body being powered by Superman's weakness the infernal do-gooder always seems to find a way to stop him and now with the Justice League it is even worse. Although he came pretty close a few years back to getting rid of Superman. Toyman had zapped him with some fancy ray gun thing-y. Unfortunately it only sent Superman to the future and not kill him like it was suppose to. Last time he works with that fruit loop. Lex Luthor on the other hand...now you are talking.

"I am still in the hallway," Metallo points out as he takes in what Lex has created. Fight fire with fire Lex said or fight Superman with a carbon copy. "Little young ain't he," Metallo remarks at the age of the clone.

"Yes but I can't risk ageing him much more without causing his DNA to destabilise. However with what I have planned it will be sufficient as long as you remember he is as vulnerable to kryptonite as his progenitor so keep your distance." It was more important than Lex was letting on that Metallo stay away. He did not have enough genetic material left to try again and another attack on Superman to get another sample would be too suspicious. Raise too many questions. Get a certain flying rodent themed hero sticking his nose in where it was not wanted and risk Lex being found before he was ready.

"So no manly hugs then?" Metallo quips. Just because he is an insane cyborg doesn't mean he has no sense of humour.

Clark reaches home and sinks into his chair with a loud sigh. Even the usual warm greeting of his children couldn't cheer him up.

"Still no sign of Lex then," Diana observes from her husband's mood.

"No," he says with regret. Clark has a funny feeling something is up. First Metallo breaks Lex out of prison and shortly after that Metallo shows up in Metropolis spoiling for a fight but with no sign of Lex. In fact there had been no sign nor trace of Lex for weeks now. It was worrying Clark. It could only mean Lex was up to something. Clark did manage to win the fight but he had been too weakened by Metallo's kryptonite heart to apprehend him so Metallo escaped and he hadn't been seen for weeks either. He peers out of the sliding glass doors that look out onto the backyard and watches the twins play. They were 3 years old now and to him were more beautiful and precious every day and he would protect them with his very life if need be.

Diana sits down next to her husband and looks where he is looking. Warm feelings flood her heart at the sight of their beautiful children playing without a care in the world. It had been worth every second of the agonising labour she had been through which she completely blames on Kal's genes. She can still remember it like it was yesterday...

"That's it your highness," Epione says trying to encourage her. "We're almost there."

Almost!!!! Diana was already exhausted as well as being in real pain and great Hera there was another one to go yet. Clark is here with her supporting her and when she finds the strength she will be castrating him for putting her through this. She could feel an irresistible urge to push and she figured that this was the end so she gritted her teeth and pushed with all she had.

Outside Hippolyta waits with Superman's mother and Donna as Diana shouts and yells and threatens to do many unpleasant things to her now husband as she gives birth to the twins. At Diana's wish the sex of the twins was unknown but Hippolyta had a feeling they would be girls. Diana had spent the last few weeks of her pregnancy on Themyscira since no-one was entirely sure just how long the pregnancy would be. A lot of it had been guess work based on how fast the embryos had been growing.

Diana had gone into labour suddenly so there had been little time to get people here. Saying that considering how long the labour has gone on maybe that was for the best. No point is having lots of people hanging around for hours on end.

Epione continues her work. It had actually been several centuries since she had handled a birth and this was no ordinary one. "Yes that is it your highness. I can see the head…keep going…there you've done it."

Diana falls backward against Clark's chest and attempts to regain her breath. She looks up at her husband. "Kal is the baby alright?" she asks in an exhausted whisper.

Clark has a tear in his eye and before he can answer the baby gives an answer by crying.

The cry reaches right into Diana's heart. "Is that my baby?" she asks in total disbelief.

"Yes it is and he is fine," Epione tells Diana as her assistant cleans the new arrival up.

"He? It's a boy?" Diana queries. She knew Kal knew because of his vision but she had wanted to be surprised.

"Yes," Epione confirms. "And you'll get to hold him soon but first we have to deliver the other one."

Diana nods and braces herself for the inevitable. At this point Donna sticks her head round the door. "I heard crying."

Diana shoots her sister a glare. "Donna not a good time," she grinds out as the urge to push rises up once more.

Clark being remarkably calm he thinks as he answers Donna's unspoken question. "It's a boy."

Donna smiles brightly and goes back outside to inform her mother and Clark's mother. "It's a boy!"

Martha is over the moon. She has a grandson. Oh how she wishes Jonathan was still here. Hippolyta on the other hand is slightly bemused by that. She had been certain it would be a girl.

The second baby comes quickly much to Diana's relief. She had been in labour for several hours and is totally blaming Kal's genes for that.

Epione cleans this one up herself but not before telling the parents of the sex. "It's a girl."

On cue Donna's head appears round the door. "I heard crying."

"You can come in," Epione tells Donna.

Donna does so followed by the 2 mothers. "Well?" Donna queries.

"It's a girl," Clark tells her.

"Alright!" Donna whoops. "Way to go sis. You managed the whole package."

"Oh very droll Donna," Diana says wearily.

The assistant hands over the first born to his mother and Diana cradles the little bundle in her arms. His eyes open and Clark who is beside his wife says the first words that come to his mind. "He has my eyes," he says smugly.

Diana is simply looking at the baby in awe. "Did he really come from me?" she asks not quite believing she had created something so perfect and beautiful.

Clark leans down and kisses her cheek. "Yes he did."

Epione has by now finished wrapping up the girl in a blanket. "Here do you want to hold your daughter now?"

Diana looks up. Her…her daughter. Oh gods this is too much. Clark meanwhile picks up the boy from her and holds his son for the first time. He looks down in total wonder at the tiny little baby. He never thought in a million years he would have this day. It had seemed so impossible as soon as he learned he was an alien. The odds he was even compatible with human being seemed so impossibly huge yet here he was holding his son.

Epione hands over the girl to Diana who is simply in awe at the stunningly beautiful little girl she now holds in her arms.

"Clark?"

Clark looks to his side and his mother has come beside him. "Hey mom. Say hello to Jonathan Kent."

Martha smiles radiantly. "You named him after your father?"

Clark nods. "Diana and I discussed names a while back and agreed on Jonathan for a boy."

"Here," Clark says handing him over to his mother who gladly takes him.

Martha looks down at the baby who she could swear was already focussing his eyes. Not possible for a normal child but this was Clark's son and she really means that because he looks so like Clark that it is almost spooky. Ok Martha never saw Clark as a baby but close enough to see how similar the child looks.

Martha walks over to Hippolyta. "Isn't he handsome?" she asks Hippolyta.

Hippolyta looks at the child and has to say he is.

"He looks just like Clark."<