Usual disclaimer, no rights to any characters portrayed.
Gathering information on the "heirs' was painfully slow, but it was coming together. Over the space of about twelve months, they had tracked down at least partial medical records for about fifty probable "heirs", and they did not tell a pretty story. Over half had almost certain terminal medical problems, and the fact that the medical issues were reduced, the younger they were, was something that screamed for attention, even though it could just be that their medical problems became more chronic after they reached their mid-teens? Something in the back of Chuck's head kept nagging him, but he just couldn't put his finger on it. As their resident medical expert, Ellie also examined the medical records repeatedly, trying to work out what she was missing.
The records that they did manage to locate made them seriously question whether the "heirs" in their mid-teens were, in fact, the youngest, given the indications were that there were initially 5 – 10 "heirs" each year and the younger the "heirs" were, the healthier they were, it didn't make sense that they'd just have stopped about 15 - 16 years ago. (What eventually came out was that the production eventually stopped about 5 years ago, Graham had funded about four years ahead and stayed away so that there were no leads back to him from the facilities, and they kept operating for about four years after he died (until the money ran out), because they were afraid to stop working until he gave orders to stop.) The prime instruments that they'd been using to locate the "heirs" (the image searches based on Langston Graham) weren't likely to get hits on boys who were early teens at the eldest, because of the changes that would happen to the facial structure between childhood and maturity, so Chuck and the others were trying to think of search parameters that would get them around that, but with little success. They did try their own variation of the FBI's software that was used to project what a face would look like at varying stages of life, but the umpteen thousands of hits they got on that meant that it would be a long time (if ever) before they got any usable results from those searches, given the rest of the variables.
In the midst of this, Yvonne and Zack had their sixteenth birthday. Their parents smiled when it was Zack who suggested that Yvonne have her Sweet Sixteen party on the Saturday and he could have some friends over afterwards on the Sunday, hopefully that meant they weren't doing too bad a job as parents when their children were this caring towards each other? Being summer, and seeing that they had a full sized pool at Castle Carmichael, Yvonne's party ended up being a pool party. While all her girlfriends were insanely jealous of how hot her mother (and sister, and cousin, and aunts, and HER) looked, and had the hots for her brothers (and father) it was going great until Yvonne turned to see what her friends were looking at, only to find that it was her parents off under the trees, making out, she watched as her father reached down to gently cup her mother's behind and effortlessly lift her with one hand (with hardly a sign of muscle action, let alone strain) to his lips for a kiss, a kiss that started out chaste enough until her mother wrapped her arms around his neck and her legs around his waist and turned it into something rather more passionate. Her friends just gasped as she coughed and said "Yeah, they're fairly affectionate." Yvonne turned away but her friends just stood and stared, eventually her mother registered that they were being stared at and looked around, quickly hopping down to straighten herself out when she saw the audience before she wandered off in Yvonne's direction, pausing to kiss her daughter and whisper "Sorry Sweetie" as she passed. It took Yvonne a while to turn the conversation away from what they'd just watched after that, but the party went on, and everyone had a good time. Chuck and Sarah managed to avoid repeat of the show at Zack's party the next day.
A week or so after the twins' parties, Chuck was winding up Casey about his taste in music when he was playing country, and it was Casey's defensive response of "Dolly's a hell of a woman" that finally made the niggle that had been at the back of his head whenever he was trying to work out Graham's "heirs" came to the fore. He broke off his conversation with Casey and literally ran off, leaving Casey looking after him as if he was crazy (not that there was anything unusual about that). As soon as Chuck was down in the bunker in front of the big screen he brought up all of the heir's medical records to compare them, after about ten minutes he called Ellie and asked her to come down to the bunker. When Ellie arrived (with Stefan, Mary, Casey, Sarah and Carina as they all knew that something was going on), Chuck asked her what the probability of multiple siblings having identical medical afflictions (waving at the screen) was, Ellie paused while she accessed the medical database in her Intersect and made a determination before giving him a response that was extremely low. Chuck nodded, still looking at her, and then asked "What about clones?" Ellie stared at him in shock before turning to the massive display in front of her. She spent about five minutes doing the same comparisons he had as she accessed what clone related information she had, before turning back to him to say that the probability for clones was considerably higher, and it was high enough to explain this (as she waved at what was on the big screen).
Ellie shook her head, asking how she could have missed it, she knew something was off but she hadn't twigged to the obvious answer, Chuck nodded, saying that he didn't click to it either until Casey said something about Dolly, and then it fell into place. Mary interjected to ask what Dolly Parton had to do with anything, so Ellie turned to her to say "Nothing, other than the fact that the first viable cloned sheep was named after her nearly thirty years ago." She went on to explain that the aspects of the medical records that had been puzzling both Chuck and herself were that they were too similar to be explained by any normal circumstances, siblings (except for identical twins, perhaps) would have some genetic variation between them, and therefore it made no sense at all that nearly all of the "heirs" had almost identical medical conditions. On the other hand, if the heirs were all, in fact, clones of one individual (Langston Graham), then it was conceivable that they would all be genetically identical. One of the key factors was how new cloning technology was, thirty years ago was the first time they managed to viably clone a mammal (Dolly the sheep), and the failure rate was terrible at that time, things had been slowly improving, but it was less than ten years ago (in China, she added, looking at Chuck thoughtfully, who nodded) that they had managed to get the process working to the point where the success rate without serious complications in pigs was over 80%, so that would probably explain why all the "heirs" that they had located so far had had so many medical issues, if they were clones it was amazing that the older ones they had found survived this long.
They all went quiet for a while as they considered the ramifications of what appeared to be in front of them, given what they knew of Graham's megalomania, it made sense that he was trying to create an army of clones of himself to run his empire. (When Sarah thought of an army of clones she suddenly went pale and grabbed Chuck's arm, asking what use would four super soldiers be in controlling the world? Chuck's eyes went wide as he realised what she was saying, once Graham had managed to successfully clone himself to run the empire, he could have cloned their children to create the army that kept the world under his thumb, that was why he wasn't worried that there were only four children in one family that came out of the second generation of his breeding program, he didn't want breeding stock, he wanted clone templates!). The others looked at them, asking what had terrified them that way, so Chuck explained as he held Sarah, who had started to cry. When he had done so the others looked horrified, but were nodding as it made a sickening kind of sense.
Given the probability of what they now believed to be the secret behind the "heirs", they resolved to track down and destroy any and all mechanisms that were being used to perpetrate this, as they now not only had to wipe out the last dregs of BGRU, they had a very real need to protect their family from this. Once they had calmed enough to discuss the situation, they called the family (except the kids) down to the bunker to explain what they had found, this time Ellie did the talking as Chuck and Sarah were at the end of the conference table, holding onto each other. The whole family was (of course) behind their need to ensure that they wiped out all records and development on Graham's cloning program. What to do about any remaining "heirs", and even more importantly, any Bartowski clones that they may have already created was a much bigger issue. Try as they might, they couldn't separate emotion from reason enough to make any decisions at that point, so they decided to put that question aside until they discovered any clones who weren't already doomed experiments.
Given the new priority, they once again put aside any government work and just concentrated on tracking BGRU and trying to locate the cloning facilities that Graham had been using, the main thing in their favour now was the fact that they knew that they needed to focus on China, and that they were, in fact, looking for cloning facilities. They also had another angle to search for, and much as they dreaded finding results on it, they initiated other searches on the childhood images of their own children.
Given that they finally had a better idea of what they were looking for, they also did more research into Graham's origins and found what they believed to be the reason behind the heirs' parents' deaths, apparently when Langston Graham was seven, his parents died in a car crash and he was adopted by another couple. Then when he was eighteen his adopted parents were shot and killed in an armed robbery gone wrong. So apparently the "parents" of the heirs were being killed in the same timeframes in an attempt to recreate Langston Graham's childhood and teenage years more authentically, which was obviously intended to mould the clones into a closer copy of his mindset through similar life experiences.
Now that they could focus the searches onto relevant criteria, they were getting results faster, and unfortunately the results that they DIDN'T want to get were what was leading them to more answers. Obviously Graham's people had managed to get bio-samples of their kids, because they were getting hits in China, Eastern Europe and the USA on children from 5-9 who were a match for Yvonne, Zack, Jaqui and Piotr, and in the same areas they were also discovering "heirs" in similar age ranges. The records that they were now starting to find appeared to indicate that the children were being born in a few facilities in China and then shipped off to foster parents as babies as soon as they proved healthy.
When they first started getting hits on their own children's clones, they sat down with the General and laid out the ground rules on what was to happen with them (as well as the Graham clones), getting the President to formally ratify the agreements once they had been made. The core requirement was that none of the clones (Bartowski or Graham) would EVER be employed in any intelligence or military capacity by the USA, or any other country that the President had agreements with (largely made up of the "team" who he'd been working with around the world to take down BGRU). All the clones would be taken when they were discovered and placed with solid, trusted families in countries where they could be protected and given the best, and most "normal" upbringing possible (Clan Carmichael would foot the bills for and watch over the Bartowski clones, the government would foot the bill and provide oversight for the Graham clones). The best that they could hope for was that the fifty or so clones of each of their children that were out there would have a chance to lead happy, fulfilling lives, but there were copious tears shed most nights in Chuck and Sarah's room, thinking about all the lost children who were, in a very real way, their's. There were less tears shed for the hundred or so Graham clones that they believed to be out there, but there were some, as they were in a similar position to the Bartowski clones.
Now that there was a plan in place to try to protect the innocent children (even the Graham clones were innocent children, they couldn't blame them for the sociopath who caused them to be created), they focused on the facilities and people who created them, and they needed an outlet for the rage that had been building in them ever since they found out about the plans for the clone army based on their children, so the existence of their new targets was going to be ending as soon as possible.
Their new resolve to wipe out Graham's cloning facilities and any record that they had ever existed was matched by their resolve to wipe out what was left of BGRU, and all of Clan Carmichael was focussed on that. As they discovered Graham's cloning facilities, CI people led the strike teams in to extract all information that they could find and any viable interrogation suspects, then the facilities would be destroyed with all personnel, the interrogation suspects would be pumped dry of everything they knew before being disposed of. They kept this up until they were satisfied that they had retrieved everything that they knew about BGRU, every shred of information relating to Graham's cloning program for the past twenty years and anything at all relating to Chuck and Sarah's children had been recovered, and that no-one outside of Clan Carmichael (aside from the General and the President) knew anything about Graham's breeding or cloning programs that related to the Bartowski children. When Chuck and Sarah were discussing these things with the General she could see that they didn't even trust her totally with this information, but having finally accepted the worries of being a mother she could relate to that, finding out that bio-samples had been stolen from their children to create a clone army of super soldiers to control the world for a megalomaniacal sociopath who had been manipulating their families for decades to create said super soldiers? She'd have trouble trusting anyone, too. (She also would have trouble believing that this wasn't all a far fetched science fiction story if she hadn't lived through it herself over the past ten years or so.)
When they discovered about the Bartowski clones they resolved to tell the kids, as soon as they felt that were ready to handle it, and they changed the Carmichael Industries direction. They obviously couldn't have one "normal" family with over 200 children spread around the world, but they could set things up so that they could be brought into the fold and looked after when the time came, if they wanted to. Therefore, Carmichael Industries was no more, and the multi-national Quantum Concepts was born, they established centres in most countries where the Bartwoski clones were being relocated to with good families, the QC centres were mostly based on smaller versions of Laputa, with extensive lab facilities added to the previous facilities, QC still did everything that CI did, but added research and development in any of the fields that they expected that their children (all of them) would gravitate to. The initial staffing of the facilities was meagre, they recruited some exceptional people in the relevant fields once they were totally convinced that they could be trusted, but they had no need to fill the ranks yet as they weren't doing much of anything other than hunting down and relocating the clones to good families, and hunting down and obliterating anything and everything that related to (or had any form of connection to) BGRU.
It took over nine months to locate and destroy everything relating to Graham's cloning program, about sixteen months to locate and relocate what they believed to be all of the Bartowski clones and most (they believed) of the Graham clones, but it was going to be years before they managed to track down and destroy what was left of BGRU, they still had a lot of very experienced operatives and directors who knew how to hide, and the rats had scurried deep into their holes.
They finally sat the kids (all of the Bartowski children including Clara and Charlie) down after Jaqui and Piotr's fourteenth birthday to tell them about the clones, they weren't sure that they were 100% ready as yet, but they had to be told before something came out. At first they didn't believe what they were being told, so Chuck went back to the start and told them (with what evidence that they had) about Graham's plan to breed the ultimate soldiers/spies via the Bartowski family, Graham's attempts to create clones of himself, the realisation that the two programs were probably related which led to the search for the Bartowski clones, and the discovery that Graham had started creating his clone army using their "perfect" genes. Then they explained the plan that they had put together in an attempt to ensure that all the clones were raised properly by good families, and the fact that Quantum Concepts was created so that the Bartowski clones could have a place in their world if they chose to. Charlie and Clara of course had questions about why all the Bartowski clones were based on Yvonne, Zack, Jaqui and Piotr, Ellie explained that Graham's breeding plan focused on Chuck as he had believed that Sarah was the only suitable candidate to extend what he'd created in the first generation of his breeding plan (pointing to Chuck and herself), if he'd found other "suitable" breeding partners for them there may have been others that he believed to be suitable to clone for his ultimate warriors, but if he did locate other "suitable" partners his plan must have been disrupted (they heard Casey mutter "By killing his ass!" but Ellie just continued), so the only ones that Graham apparently believed to be suitable for cloning were the second generation of his breeding program, waving to Chuck and Sarah's kids. Charlie asked what other plans that Graham had had for them, but when he saw Ellie glance toward Clara and blanch, he withdrew the question. When they finished and the others were leaving to think about what they'd just heard, Ellie put her hand on Charlie's arm to indicate that he should stay, when it was just them, Chuck, Sarah and Carina, Chuck closed the door and sat down again.
Chuck went to start the explanation but Ellie just held up her hand to him, so he sat back and waited for her to be ready to tell the story. When Ellie had composed herself enough, she explained to Charlie that she (they, when the others went to say something) didn't want Clara, Yvonne or Jaqui to ever hear about the specific plans that Graham had for them, but they wanted him to know so he understood what the family was up against. Even though Clara was older than he was, Charlie was really the leader for his generation of the Bartowskis. Charlie started to say that he didn't want her to tell him if it upset her that much, but Ellie shook her head with tears in her eyes, saying the he needed to know. With that, she drew a breath and told him what Graham had told Chuck, Sarah and Mary about his plans to "train" and use Yvonne and Jaqui, and what "Bella" had told Sarah and Carina about his plans for Clara. Charlie just sat there with tears in his eyes, utterly horrified by what he was hearing. Chuck brought up the transcripts from Bella's interrogation to show him what was actually said about their plans for all of them, including himself, to give Ellie a chance to compose herself (talking about a monster's plans for your daughter and nieces is not something that most can do without being seriously affected), and when she was able she continued, explaining to Charlie that they needed someone in his generation to understand what they were up against, and unfortunately he was the only one bright and mature enough to handle that responsibility, they needed him to look out for Clara and his brothers and sisters and steer them in the right direction when they couldn't come to their parents, and down the track, he would hopefully help his other 200 brothers and sisters if they chose to join the family when they were told the truth about their situation. Chuck took up the explanation there, telling Charlie about what precisely they were setting up with Quantum Concepts, and how they hoped that they'd be able to bring the others into the family via QC when they were old enough to know the real story. Charlie looked around and said that he'd do his best, and after they lined up to hug and kiss him (and apologise for putting something like this on him), they all went upstairs. Chuck held back and when it was just the two of them asked Charlie if he was sure he was OK? When Charlie said that he was Chuck hugged him again and they left to join the others.
A/N: Send in the clones, it would have been easier to just say that the "heirs" were clones up front, but where would the fun be in that? Hope the build up wasn't too boring for most people.