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 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 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."

Donna is there also and remarks "You're right. I even think he has the same dimples."

"Do you want to hold him?" Martha asks Hippolyta.

Hippolyta hesitates at first but she doesn't want to appear uncaring simply because the baby is male so she gently takes the baby from Martha and looks into the innocent blue eyes that seem to be regarding her with wonder and her heart melts. She hasn't felt like this since the days Diana and Donna were brought to life.

"Hey," Clark says getting Diana's attention. "Look," he says indicating in Hippolyta's direction.

Diana looks and she smiles. Her mother is staring in total love struck awe at her son. She is so pleased that her mother seems to be accepting of her son. "Mother?"

Hippolyta looks at her daughter.

"Do you want to hold your granddaughter now?"

"Oh of course," she says while uncertain what to do with her grandson. Donna comes to the rescue since she hasn't held him yet.

"Hey there," she says once she has her nephew. "I'm your auntie Donna and you young man will be breaking many a female heart once you are grown up," she jokes. He was already impossibly cute and considering whose genes he possessed Donna's joke will probably turn into a reality.

Hippolyta moves over next to her daughter and takes the newest baby and almost gasps.

"Mother?" Diana queries.

"She looks just like you did."

"She does?"

Hippolyta nods. The resemblance was remarkable except… "She has the father's eyes."

Clark smiles smugly. "Wow two for two."

Diana rolls her eyes and shakes her head. She will never hear the end of this now. Clark had already spent her pregnancy jokily boasting about how smart the twins would be because they had his 'superior' genes.

"What is her name?" Martha asks the proud parents.

"Lara," Clark answers. "Her name is Lara."

"It's days like this where I fear for them most," Clark tells his wife with real concern snapping Diana out of her reminiscent. He has always been afraid that one of his enemies might figure out who he is or if not that at least that he and Diana were a couple and from that why she had been absent from the world for over a year when she was pregnant and for awhile after she gave birth. He knows that his enemies would not think twice about using his children against him or worse. If anyone ever harmed them Clark isn't sure he could keep to his vow to never kill.

Diana takes Kal's hand into her own and strokes the back of it with her thumb. "I know but Lex doesn't know a thing about our children Kal. We've done a good job in keeping it secret," she says in an attempt to reassure him.

Clark has to concede that up to this point yes they have. It isn't always easy. It means absolutely no displays of public affection when they are being Superman and Wonder Woman which isn't as often as it use to be he has to admit. Caring for two super powered children meant reducing the workload as much as they could. They were down to being on the League reserve list which meant they were only really to be called up when there was a global, end-of-the-world emergency. Clark did find the time to do a quick circumnavigation of the globe now and again but mostly he kept to Metropolis to be near his wife and children.

Diana still had her duties. She was still Princess of Themyscira. Sure the ambassador role had been handed over to Donna who enjoyed it far more than she let on but Diana still had functions to attend and her charities to look after. It meant unfortunately time spent abroad away from her family. It was just right now with Lex loose she felt she needed to be near her children and her husband. Her time as Wonder Woman was obviously reduced but if she was really needed she was there assuming they could find a willing and trusted baby-sitter on short notice.

To compensate for the fact that Clark and Diana were not around as often the League had been adding younger heroes to the roster like Bruce's one time protégé Dick Grayson aka Nightwing and his current girlfriend Koriand'r of Tamaran, better known as Starfire. There were others as well. The former Teen Titans were definitely not teenagers anymore. All these youngsters, however, were starting to make Clark feel old even if he didn't look his actual age of 43. Of course he had missed quite a bit of them growing up with having been away in space on his futile trip to Krypton. It did make things seem odd for awhile after he got back. He had been in stasis so had not noticed the passage of so many years.

Diana takes his hand and pulls him up which brings to an end his inner musings. "Come on. Dinner isn't for half an hour yet. Lets go play with our children," she orders knowing that always makes Clark feel better. Even though she is worried too about Lex being free she has faith that they'll find him and put him away before he can finalise whatever scheme he is concocting this time. Besides she still has to get some payback on Metallo for roughing Kal up. She had felt really angry when he had come home that night covered in bruises. She knew perfectly well that they would be completely healed by the morning yet it still didn't prevent the way she felt. She had also given Kal a piece of her mind for being so pigheaded as to fight Metallo alone when he knows perfectly well what that does to him.

They wander out into the garden into the brilliant sunlight on what is a beautiful day where Clark instantly brightens up as he plays with the children. The sight is one that always brings a smile to Diana's face. She frowns as she can see them whispering together. What are they up to?

All 3 look at her with the same mischievous expression. Oh no! "No," she tells them.

"I think yes," Clark contradicts his wife. "On 3 kids. 1. 2. 3! Get her!"

Diana soon finds herself being chased around the garden by her husband and children laughing like a child herself not caring in the least that it might look inappropriate for a princess because it looks just right for a mother.

"What is your name?"


"What is your purpose?"

"To assist you in freeing the world from the tyranny of the Justice League."

"Do you know what you are?"

"Yes. I was created from Superman's DNA so that I would possess his powers allowing us to fight him on equal terms."

Lex nods satisfied. His synaptic imprinting technique had successfully instilled basic knowledge into Kon-El. It was a remarkable achievement even if he does say so himself. "So what do you think Miss Waller?" he asks of his observer.

"Satisfactory," she says as way of an answer trying not to show either way how she felt. Amanda Waller, a member of project Cadmus, looks on dubiously. Project Cadmus had been created in response to the growing Metahuman population to look into methods of controlling them should they turn against the government. Upon the formation of the Justice League a remit to find ways to counter them should they ever go rogue was added to Cadmus' charter as well. Unlike her superiors, though, she was not at all enthralled with the prospect of allying themselves with Lex Luthor. She had read his physiological profile and could see the danger signs a mile away. Luthor was border line psychotic at best and considering the actions he had undertaken in his attempts to destroy Superman before, one of which would have virtually wiped out the United States and its citizens whom she had sworn an oath to protect, she had serious misgivings about this venture.

Luthor had no morality as far as she could tell. Yes she may work in murky places but she cares whether innocent people get hurt. Luthor doesn't and his latest idea, creating a clone of Superman, was not one she was comfortable with either. Cadmus had tried and failed to do that themselves. Sure a Kryptonian being on their side would be an immense asset. The problem here was that the clone was not under Cadmus' control. It was under Luthor's. Part of her was tempted to tell her superiors that they should just throw Lex back in jail and throw away the key.

Lex could tell that Miss Waller was not overly thrilled and frankly neither was he with this alliance but Cadmus had provided him with the money and equipment he required to successfully achieve this.

"Not to doubt your imprinting technique Luthor but what happens if it fails?"

Lex should be offended he supposes but he isn't. These government types always want their little back-up plans. "This clone possesses all of Superman's strengths and his weaknesses. Kryptonite is as fatal to Kon-El as it is to Superman."

Amanda Waller nods. "I assume you came up with the name."

Lex smiles proudly. "Well I don't like to toot my own horn but yes I did. It's good isn't it."

Amanda Waller makes a non-committal noise. "I am still waiting to know how you managed it when our best scientist couldn't."

Lex laughs scornfully. "Those so called scientists are idiots while I am a genius and Miss Waller do you seriously expect me to simply hand over my only leverage on you. What is to stop you trying to return me to jail once I give up that secret?"

She thought he might say something like that. In that case she will just have to play along with him for awhile. "We would like some tests performed to confirm he is as you say he is."

"I expected that. That is no problem."

"I will consult with my superiors and let you know when so we may observe."


With that Amanda Waller departs and Lex watches her go. He'll play along for now simply because he doesn't need Cadmus as his enemy at this exact moment but they too will be dealt with in time along with any other who might threaten his plans.

"Father?" Kon-El queries from his poistion sitting on a chair.

Lex smiles at the father remark. He had programmed it into Kon-El's mind to see him as his father. "Yes my son."

"Why do I have to perform tests for that woman? I thought we had already established that I possess the powers of a Kryptonian." Since his awakening a few days ago his father had established that Kon-El does indeed seem to possess all of the abilities of a Kryptonian with the exception that Kon-El had not been able to figure out how to make himself fly but his father believed that that ability would manifest itself in time as well.

"Politics," Lex answers simply in response to Kon-El. "We need her to be an ally for the time being."

"I do not understand."

"You do not need to for the moment," Lex tells Kon-El. He shakes his head. Kon-El's knowledge base was still too basic. He would have to work on that.

Kon-El feels that perhaps he should need to know but if his father says not then he would accept that. "As you wish father."

Lex looks over Kon-El. "You know I think you need a name for when our friend from Cadmus returns. I know these government types. They love to name things."

"Name father?" Kon-El queries perplexed.

"Yes like how your other father is called Superman even though his name is Kal-El." Or Clark Kent Lex silently adds but Kon does not need to know about that and neither do Cadmus. That is knowledge for him and him alone to be used when the time is right. He looks at the boy and he is still only a boy, perhaps 15 at most in physical age and an idea strikes him. "I know. We'll call you Superboy."