OK, there's something in this one that doesn't have anything in the series to directly support it, except for the notable gaps, and the fact that someone obviously didn't get what she was from one parent.
Usual disclaimer, no rights to any characters portrayed...
After a couple of months of monitoring for all the usual suspects, and sifting through the computer disks, device logs, paperwork etc that had been collected when the teams moved on the BGRU sites, it appeared that they may have accounted for about half of what was left of BGRU at the time (not the three quarters that was reported, which was in an of itself a rather significant worry as it showed just how compromised the organisations that they were expected to rely on still were). They organised a few other mop up operations but the result wasn't significant in regard to reducing the size of what was left of BGRU.
Of course, after the operation they launched against Quinn and co, Chuck and half of the "family" was back to having trouble sleeping due to what they'd had to do in the strike against Quinn's operation, so Chuck had company working out and sparring down in the bunker at night (including Sarah quite often). The fact that their endurance was significantly increased now by the Intersect meant that they had to work harder to wear themselves out enough to sleep, but that just meant that they were getting taut and terrific that much faster (Molly was actually getting jealous that the older generation were so much tighter and hotter than she was as a teenager, so she started working out with them, well she tried to though she didn't have a hope of keeping up with them).
Given that they had been primarily targeted via the Carmichael Industries offices, they decided that, rather than re-open those offices, it was time to get rid of them. Therefore they removed all of their special equipment and sold them off to the government via the General, as it was a perfect setup for an operations office, and the security and technology features that made it perfect for that would have raised questions if it was sold to civilians (and they really couldn't keep blowing up their operations centres to cover up the evidence as that WOULD raise questions in the wrong places).
They replaced the CI offices with a large hanger building at the nearest airport that was big enough to handle the SonicStars at full take off load. It cost quite a bit to build a structure that size to their security and operational specs and have it fitted out for the operations that were required, but they certainly had the funds, and it was a better solution overall for them. They really had no need for formal offices, or for that matter a formal company, any more as what work they did now was 100% government related, and if they had any need for face to face meetings they'd go to them. Therefore, having a secure hanger for their fleet of aircraft (with room to spare for other transport planes), which also held operations centres etc and could house strike teams of over a hundred comfortably for whatever period required made rather more sense than maintaining a "front" office which basically just painted a target on their backs. The fact that it was located close enough to Castle Carmichael that they could get to and from home quickly was another bonus. Of course, most of the Clan missed the significance when Chuck named the new centre "Laputa", but Sarah had been subjected to enough of his viewing tastes to get it, and call him a dork.
Given the amount of BGRU that appeared to be left, it was obvious that they wouldn't be able to back off too far from being operationally ready any time soon, but they were out of immediate danger, so it was the opportunity for those who wanted to step away from the action to do so. Kathleen did get her Intersect backed off to the DMI version, but she kept up the operational training and made sure that it was understood that she'd go back to the full action capability if and when it was required. Ellie, Stefan, Jeff and, surprisingly, Emma, went another way (but still under the same understanding as Kathleen), they all had most of the action database removed, and Stefan, Jeff and Emma had their Intersect versions brought up to the full versions for the data processing then had the intel sections of the Intersect database loaded, which meant that they all had the equivalent Intersect resources to Chuck, Sarah and Ellie for utilising the Intersect data, Stefan and Jeff of course were already primarily working in that space, but Emma had been contributing more and more in that area in recent times.
In the aftermath of the Quinn exercise, once all the panic of locating the BGRU bases etc was over, Emma had sat down with Sarah and Chuck to fill them in on the periods where she'd been missing from Sarah's life. It was Sarah's first time hearing what Emma was telling them, and Chuck said that he'd let them discuss it alone, but both of them said "No!" simultaneously, with Emma going on to say that Chuck was Sarah's life now, and he deserved to hear it from her, rather than make Sarah try to explain it to him later. Sarah just nodded as she said that and held his hand tightly to prevent him from leaving. Emma looked down for a minute or so to compose herself and then looked back up at them as she began to speak.
She started by telling them that she had actually been working with Jack on his cons up until after Sarah was a toddler (she'd long since stopped hesitating when she said Sarah, even when she was talking about her childhood, she WAS Sarah to her now), and she'd generally been the one who did all the organisation and planning, to try and keep him out of trouble (she looked up at Sarah and said with a smile that her father had always been more of a charmer than a thinker, Sarah nodded with a little smile). When Sarah was about three or so, one of Jack's cons went terribly wrong because he'd gotten too ambitious and when it came crashing down he ran, not checking on where she was until he was out of town, but the problem was that he hadn't let her know that the con was blown, so she had no idea that she needed to run until it was too late and she was arrested.
While she was in custody, a man came in who said he was from the government. He went over the evidence of what had been done to set up the con and asked her about what parts she'd contributed to the planning, when she admitted that she'd done pretty much all of the planning he proposed a series of scenarios to her to see what solutions she'd come up with for those scenarios. They were in there for a few hours running those scenarios, and in the end he said that he could get her out of her current predicament if she did some jobs for the government (at this point Sarah and Chuck looked at each other, and Sarah told her mother that she had some things to tell her when she was finished, too, Emma just nodded), anyway, as she had Sarah to look after, she was prepared to do whatever was necessary (within reason) to prevent being taken away from her, so she'd agreed to take what he was offering.
They set it up that she would go back to her "normal" life, so long as she never said anything to anyone about the deal she'd made and she was never part of Jack's cons again. She'd be called to go away for up to a couple of months at a time to work on assignments and she'd stay locked up in the government facilities for the duration of those assignments. From then on she was called away three or four times a year to work for them, and then she'd go home again once they released her. That was why she was away those times that Jack took Sarah away with him to help him on his cons. Anyway, after the last time that he took Sarah away and they didn't come back, Emma had used her connections to get a new identity and slipped away, contacting her mother for news of Sarah whenever she could and arranging a contact mechanism via her. Sarah looked at her and asked what work she'd done for the government. At that Emma said that she wasn't a spy or anything like they were, she hesitated and then said that she was mainly doing the type of analysis that she'd been helping with here recently, which was why it had came to mind, that was over 20 years ago but it was all so familiar when she started working on the problems with them. (Emma shook her head then, saying that she seemed to be remembering more, and thinking more clearly lately, perhaps that was why she started noticing the things that she did and bringing them up, but then she shook her head again and said that it was probably just her imagination.) Chuck asked if she knew who she was working for, but she shook her head to that, saying that she would be picked up in a van or something and taken to some facilities that were god knows where, she'd be instructed to call the people there Mr Brown, Mr White, Mr Smith or something similar, and when the assignment was finished she'd be taken back and dropped off somewhere that she could get home from. Chuck and Sarah looked at each other again and Chuck asked for all the names she'd been known by up until she was arrested and when she was working for them, noting them down and giving them both a hug and a kiss before he went off to do some research, while Sarah filled mother in on her own very similar story about how she was roped into working for the CIA (leaving out those elements that she'd told Chuck that would horrify her mother and break her heart).
Chuck came back about half an hour later, confirming that Emma had in fact been coerced into being an off the books CIA analyst by one of Graham's predecessors, and by the way, the CIA had been very impressed with the work that she'd done for them, the reports had been quite glowing about her ability and solutions. He started to say something else and then stopped, Sarah and Emma both looked at him and when he didn't continue Emma said "Say it Chuck." Chuck looked down for a bit before raising his head to look at them, telling them that the reason that Sarah had been on the CIA's radar was because of Emma's exceptional ability, they had been monitoring her to see whether she would turn out to be another prodigy like her mother.
At that Emma broke down, saying that it was her fault that her baby had been dragged into that world. They both went to her, telling her that that wasn't true, Chuck put his arms around her while Sarah knelt in front of her, holding her hands. Sarah pointed out that it was Jack that handed them the means to get to her, if he hadn't kept trying his scams and screwing up, the CIA wouldn't have had a way to get their hands on her and force her to do what they wanted, so in fact it was Jack's fault that they were both dragged into that world. She looked up at Chuck and then back to her mother as she also pointed out softly that if she hadn't been dragged into the CIA she wouldn't have met Chuck and they wouldn't have the family or life they had at the moment, would they? Emma smiled through her tears at that and buried her face in Chuck's shoulder as she cried herself out.
When she had settled down a little, Chuck said that it had explained one thing anyway, they both looked up at him with questioning eyes, so he continued, saying that Sarah was brilliant, she could pull the situation apart, analyse it and plan an operation better than just about anyone (except you, interjected Sarah with a smile), and that ability never made sense when he looked at her father, but finding out that her mother was one of the CIA's better kept secrets as a highly valued analyst, that made much more sense. Sarah nodded with a smile, agreeing that she certainly didn't get her brains from her father but stopped and looked back to him, saying "But he's a hell of a dancer", which made Chuck grin. Emma smiled and said yes he was, but obviously she was missing something here? Sarah apologised and told her about Chuck meeting Jack for the first time, and how that line had come out, which managed to make Emma laugh.
When he had a chance, Chuck took Ellie aside and asked her to start re-testing everyone (including full scans), and to start with himself, Emma, their father, and Sarah (and Jeff, he added a few seconds later, realising that if they were checking to see whether previous damage to the brain was being remedied, Jeff would be a likely candidate. He may not have had the intersect in his head, tearing up pathways and overloading areas of his brain, but he'd certainly done a lot of self inflicted damage), he told her what Emma had mentioned when she was talking to them and said that it would be very interesting to see what, if any, difference there was between the pre-Bartowski Intersect tests and the Post-BI tests. Ellie nodded with a thoughtful look, saying that if there was a notable difference it would be worth making the tests a regular item for everyone to track what changes were occurring, then looked at him and told him she'd get onto it.
The changes of Intersect focus that Ellie, Stefan, Jeff, Emma and Kathleen had taken on made the others think about where they wanted to be positioned now. Given that they'd had the Intersect for months now and it was sitting comfortably, Mary and Carina decided that they'd like to see how they went with the full version, as the access to the Intersect intel was something that they saw as quite valuable, given that the majority of what they did nowadays was more analyst than operative related, so Stefan worked up the changes to the Intersect software and prepared a version of the Intel database to be added for them, and once they were loaded, optimised for them and acclimatised they could add more of the intel database as a staged approach. It took them a while to get used to the extra load and functionality, and Mary in particular found herself quite often looking at her son, wondering how he could have handled having several times this much in his head and staying sane all that time, especially when it was the earlier, rougher versions of the Intersect than the one that Stefan and Ellie devised that he'd been using in his head most of the time. Stefan watched her sometimes when she was looking at Chuck like this and one time he leaned over to her and said quietly "That's why I always said he was special, because no-one else could have handled it".
One advantage that CI still had was that at least ten to fifteen of the BGRU "party rebels" were still out there, so they were still getting hits on various locations when these guys would defy orders and go out, this was a major win for the monitoring, because the rest of BGRU had really done underground, other than the rebels they weren't getting more than a hit every week or two worldwide. The intel they got from the last mop up operation helped them narrow down the locations of the last BGRU bases, and they were running their usual real estate, utilities etc searches in an attempt to nail them down. They were also intensifying the satellite imagery and security camera scans for anywhere they believed that there was a BGRU presence, they were getting some hits out of that, but not many. That wasn't so surprising, given that what was left of BGRU was in a panic and going deep underground to try and prevent discovery.
With the rarity of hits on the BGRU "people", it was a major shock when a hit came up on a name that they KNEW couldn't be alive, because Chuck and Sarah had shot him to pieces, literally. But for all that they were seeing both the name Langston Graham and a face that certainly looked like his up on the displays. They scraped all images relating to the hit and put them up on all the available screen real estate, in the process they found a few more known BGRU faces in the background, so that confirmed that it was still related to the organisation. Their first thoughts were that someone may have dug up a Graham look alike to parade around and use as a puppet to gain control of what was left (a puppet for the puppet master, that was interesting?), but when they analysed the images they realised that it was a much younger man, probably in his mid to late twenties, so that couldn't be right. The reason that they hadn't picked his age at first was that there was something definitely wrong about him, he looked far too worn out and haggard for a man of his age, and he moved like a geriatric. One thing WAS obvious, though, he was most definitely related to Langston Graham, not just because he tripped the image recognition programs for Graham, but also because most of his mannerisms were Graham's, too. The only thing that they could think of was that this man was Graham's son, even though there were no records of Graham having a son. Chuck broadened the parameters on the image recognition software and ran the search for Graham again over the real time and archival records, trying to get a better idea of where this man came from, and why he had suddenly turned up in South America.
With the looser search parameters, they of course got thousands of hits on the possible Graham images, so they sat down to do what Chuck and Sarah had done when they were searching for his father, go through them one at a time and flag the ones that looked promising, then go through them again, looking closer until they were relatively certain of what they had. At least they could share the load across the team this time, so it was much easier and quicker. The first cut reduced the pool to 4-500 images and videos, the second took it down to about a hundred and fifty, the next to fifty, but on the final cut they still had about twenty images that looked solid, and the problem was that they obviously weren't of the same man. What they had was images of possibly ten to fifteen different men ranging in age from the first one they'd found (possibly late twenties) down to mid-teens. The images were from South America, Eastern Europe and China, for some reason. There were only two who appeared to be in their twenties, and a few more in their late teens, the rest seemed to be in their mid-teens. Another thing that was strange was that they all (the older ones especially) seemed to be sickly and, well, "wrong", there was definitely something not quite right about them. The only concept that seemed to make any sense was that Graham had initiated another breeding program, this time using himself as the focus. Presumably he'd been spreading his seed via artificial insemination and surrogate mothers to ensure that he had heirs to take over his empire when he was ready to step down.
The sickly state of all these men made them wonder whether there was some serious genetic defect in Graham's family tree, Graham had always seemed quite robust, but all of his sons (they presumed) appeared quite frail and struggling to manage. Given the sound scientific basis that had driven the Bartowski breeding plan, it seemed strange that Graham wouldn't have taken similar measures to ensure that his own heirs were as healthy and sound as they could be. The fact that they'd never discovered anything about Graham's sons in any of the BGRU files was another conundrum, as you'd think that he would have put measures in place to ensure that they were looked after, education, support, protective details, all of the things that you'd expect to find in spades for the heirs to the empire had been totally missing, even from Graham's private files. For that matter they hadn't even found any indications that he'd visited or communicated with the BGRU (or any other) facilities where they'd found the heirs.
To get to the root of the matter, they initiated searches to try and identify and back track these men, in hope that they could uncover what Graham's plan actually had been, and why he had gone to such lengths to keep their existence a secret.
While all the research about Graham's heirs was going on, Ellie completed the testing and scans on everyone that Chuck had requested, so they sat down (with Sarah, as she was the only other one across this as yet) to go through the results, and the comparisons with the pre-BI tests and scans (luckily Ellie had insisted on full scans for everyone before they had any significant procedures, because she wanted to ensure that she had every piece of information available to evaluate the risks before she allowed anything to progress (well, except for Stefan, but they did have all the tests that she'd been doing on him to keep track of his progress and condition back to when they suppressed the Intersect in him when they recovered him from the Russian Intersect facility), and she had missed some of Chuck's scans prior to the load of the final version, but she also had a scans on him gong back years as she'd been monitoring him and Sarah along with their father). The results were quite interesting, as there was a clear indication in nearly every case that any evidence of damage or trauma was reduced after the BI was loaded.
In their father's case, the indicators that they'd associated with Intersect activity and damage (from the very rough early version that he'd loaded into himself while he was developing the Intersect) were largely repaired, and so was the other damage that they presumed was a result of his death and the Ring's revival process. In Sarah's case, the damage caused by the flawed Ring Intersect that she loaded and Quinn intentionally overloading the Intersect in an attempt to burn out her memories of her life with Chuck were also showing signs that they were largely repaired (Chuck beamed and squeezed her hand when they looked at these results).
Looking at Chuck's scans, they saw more evidence of damage and trauma than on anyone else's. It was clear how much damage the early Intersect versions caused (Version 1.0, the Fulcrum Intersect that burnt out the brains of everyone else who it was loaded into, Version 2.0 before the governor, and probably that very early version he loaded when he was six), and also the separate and quite distinct damage caused when the Belgian's scientist was trying to erase his memories and personality to unlock the Intersect, but in his case as well, much of that damage appeared to be being repaired.
When they got to Emma's results, they looked for evidence to support Chuck's theory that it may have been the BI which prompted her to remember her previous life as an analyst, over 20 years ago, and improved her abilities in this area. Emma's pre-BI tests didn't show any significant damage or trauma, she hadn't led the crazy life that the rest of them had and hadn't damaged her brain through her own or other's efforts, but the pre-BI scans did show "dead" areas that may have degraded through age or other reasons, and it was apparent that these "dead" areas were also being repaired post-BI, so it appeared to be reasonable to presume that the BI had, in fact, "fixed" the previous lapses that she had.
When they'd gone through everyone's results and had seen improvements on some level in every case, they sat back and looked at each other. Quite aside from any other aspect of the BI, and it was by far the most powerful and effective version of the Intersect that had ever been created (not surprising, considering it was the only version that was ever designed and created by the original designer (in partnership with his brilliant Neurologist daughter and equally brilliant son) without any interference from outside parties with hidden agendas), the BI was apparently also an incredible healing tool that repaired and enhanced the host's brain and body by triggering its innate repair mechanisms while it was operating. As a medical professional and scientist, Ellie wanted to publish these results for the world to see, but she knew that she couldn't, as they couldn't let the world know about anything this powerful. Chuck and their father had been hunted and/or tortured to get the Intersect for the entire time the outside world knew that it existed. They only dropped off the radar when a) the rest of the world was convinced that their father was dead, and b) the people hunting it were assured that it had been removed from Chuck's head. If word got out that they'd recreated the Intersect, and that they'd created the ultimate version, none of the family would ever be safe again.