Usual disclaimer for the land of litigation, no rights to any characters portrayed.
Chuck eventually found the genetic analysis for Sarah buried in Graham's files, and as expected Sarah had the same Beserker genetic markers as he and Ellie did (and to a lesser degree their father, Chuck was still hunting genetic records for his mother, but the margin that he and Ellie had over their father father implied that their mother also carried the Berseker genes to a degree as well, which could also explain why Mom was such a bad ass herself). They had yet to work out what the actual differences in the neural pathways that made them better Intersect hosts were, but that was Ellie's speciality, she was the neurologist, and she was working on it. The main thing that Chuck got from that was Sarah and the kids should be safer if they came in contact with the Intersect, and that their kids WOULD be little superheros (though they didn't wear capes much). Basically, the signs were there already, but there was every reason to expect that their kids would at least match Sarah's fighting etc abilities, possibly even exceed them as they had the genes from both sides. Given the fact that they now knew that the family would be at risk for years, if not forever, that gave Chuck and Sarah a small amount of comfort, and Sarah concentrated on training the kids as well as they could to look after themselves, while still trying to make it fun because, well, they were kids.
Even though Chuck hated Graham and everything he'd done, he had to be impressed (from a purely scientific viewpoint) with the ground breaking scientific analysis and planning that had gone into the breeding program that they were all part of. They'd managed to identify and isolate the gene markers to get the specific attributes and outcomes that they wanted thirty five years ago, and then engineered the situations to put the people with the best mix of those gene markers together to procreate, he'd never heard of pure science being used in human genetics that way before (possibly because it was so inhuman, unethical, illegal and just plain WRONG?)
Stefan and Ellie were working together on the Intersect whenever they had a chance, trying to optimise it for the human brain, and in particular the Bartowski brain, as an optimised Intersect would give them their best chance when people came after them. Chuck was the obvious guinea pig for this as he was proven to be the most resilient person alive (if not ever) in regard to the Intersect, and all testing would be done on him. He put his foot down when Sarah suggested (or more to the point, insisted) that she share the testing, as that would put risk on both of them (not actually mentioning the kids but leaving the need for them to be looked after hanging over the issue), and he wanted to make sure it was safe before she tried it. As usual she wasn't happy about him taking risks, but conceded his point in this instance.
With everyone settled into the revised Castle Carmichael now, it was amusing how "normal" the spy clan looked sometimes, Ellie, Carina, Kathleen and Emma now had their own "special" Odysseys too (well actually Kathleen and Emma's were Chuck and Sarah's original pair, the new batch were uprated in performance, armour and armament, they could handle 25mm bombardments and the Thumpers now each carried a cylinder of rounds and a pair of SAW versions of the CI assault rifles each carrying about 3 times the ammo of the assault rifles in a pair of axial mags, and Sarah and Chuck could make use of the extra capabilities far more than the Clan's civilians) and each school day there were two carpooling trips to school, one would drop off and pick up Yvonne, Zack, Jaqui, Piotr and Wendy, and the other would drop off/pick up Molly, Clara, Charlie and Susie. (One drop off/pick up would always be Sarah or Chuck, the other was usually Ellie or Carina.) For all their "normal" appearance, they certainly had enough armoured vehicles to carry everyone safely now, with the six Odysseys, three armoured SUVs and Casey's Crown Vic (he'd never give that up), but of course they also had Sarah's Shooting Brake, Mary's SportBrake, Zondra's (previously Sarah's and Carina's) Lotus and a few other flashy sporty cars that were more in keeping with the expected image.
With BGRU's back broken, Carmichael Industries was once again taking on contracts and going back to work, they were still putting a fair bit of effort into the mop up exercise, and that would be an on-going thing, but they were starting to pick their "normal" lives up again. With Bella gone, the General organised for a few new CI "staff" that she could personally vouch for. Of course, she had a secret plan which she had cooked up with Casey to select those "staff". Given that Alex and Josie's relationships hadn't panned out, and the situation was less volatile now, the single girls (Zondra, Heather, Josie, Alex and Ellie) had started going out partying and playing up again, and that worried their parents no end. Therefore, it wasn't a coincidence that the "staff" that the General organised for CI were made up of the type of gorgeous and nice young guys that she and Casey would like to see their daughters with, how that would pan out, especially as both daughters were quite bright enough to see through what they were doing, was going to be interesting to watch.
A few months after the (new) incident with Sarah's dad, they got hits on the ongoing BGRU scanning that indicated that Riley and the Ring Director had popped up in L.A. (along with Jasmine, who apparently hadn't died when they blew up Hartley's mother's house, or more to the point, she blew up her house to get Volkoff's people) while Riley was Volkoff's minion, and the Director was the Ring elders', they had been significant parts of those organisations, managing and running them to a large degree, so those two rated considerable attention and suspicion, and Jasmine was a dangerous and resourceful operative as well. So Clan Carmichael was back on alert while they sorted out what these people planned to do, and how to deal with them.
The kids (especially Molly) would have been mortified if they realised that they were being tracked and monitored every second that they were outside Castle Carmichael, but ever since the BGRU situation came up, everyone was, the girls had tried to insist that the monitoring be dropped when they were out partying but they finally caved in when they had to accept the very real risks they were all under. While the girls could understand the need to monitor, the kids wouldn't (especially Molly who'd been leading the life of a fairly normal teenager up until Jack screwed that up for them), so the "big screen" in the bunker normally displayed live security camera footage of them (and anyone else when outside) showing wherever they went, using a mix of their tracker signals and image recognition to ensure the best camera coverage (a slight modification of the algorithms that Chuck had created years ago to search for people).
Sarah would often watch Molly on the screens with tears in her eye, happy that she was able to be a teenager, and see her being happy with her friends (and boys), but at the same time sad that they needed to watch over her this way to keep her safe. Chuck would often come up behind her and hug her when she was like this, knowing that part of what she was thinking about was the sacrifices that she and Emma had made to give Molly a normal life, only to have that ruined by her father's selfish attempt to look after himself, as usual. Sometimes Chuck could make her laugh, like when he said that this gave the term Big Brother a whole new meaning (she had managed to give herself a proper education, in spite of her father's attempts to the contrary), other times the attempt fell flat, like when he mentioned how much harder it would be with their own girls and Clara, as Molly was a pretty enough girl, but no beauty, but their girls took after their mother, so they would be stunning beauties, as would Clara. Chuck and Casey had already scared off a string of would be boyfriends for Molly because they'd seen what they got up to with the girls, no it would NOT be fun when it was his own daughters or his niece.
Watching what the boys at Molly's school got up to was what led to her finding out that she was being monitored, she was being chatted up by one of the serial seducers one day, and she was just at the point of getting into his car when Sarah called her phone to tell her that if she got into that car she'd be grounded for the next ten years at least. Molly sparked up and started arguing with Sarah, but when he tried to force her into the car the defence training that they'd engrained into her kicked in, and she broke his arm in three places, smashed his knee and ensured that he wouldn't be seducing any girls for a long time, if ever (ruptured testicles has that effect). Sarah got there at that point and whisked Molly away in her Shooting Brake, and when the boy's parents tried to get Molly expelled and sue them for damages, Sarah, Chuck and Emma had a meeting with them in the principal's office, where they showed them and the principal footage of what actually happened, and also footage of the other girls he'd forced into sex on school premises (as well as others he'd taken away from the school, like Molly, presumably to do it somewhere else where he could control them). At that point they started to threaten to sue for breach of privacy, and called Molly a slut who already had a reputation and Chuck smiled, the father jumped up and wanted to go at it with him, then and there, and was even more infuriated when Chuck shook his head with a smile, saying that his wife would kick his ass if he got in her way at that point. Sarah was on her feet by then and quietly asked the father whether he accepted responsibility for making his son into a copy of himself, a sleazy rapist who preyed on innocent girls, which was enough to get him to attack her. Chuck did jump up and stop her when she was about to finish him, to prevent the situation getting serious, she'd done much more damage to the father than Molly had done to the son, but the principal had witnessed him attack her first, which meant that she clearly did that in self defence. If she killed him it would have been something else, so when Chuck saw the moves leading to that start to form, he jumped up (faster than the principal would have thought possible) and grabbed her wrist, pulling her into his embrace as she started to cry. They left the footage with the principal and the school contacted the parents of those girls to explain to them what had happened to their daughters, as Chuck had told them to expect, on the basis of the patterns witnessed, the girls had been threatened with physical harm and/or being outed as serial sluts if they'd told anyone (including the parents), so a number of parents only found out how their daughters had become to be pregnant when they were contacted by the school. The only upside of that experience was that Molly became very popular with the girls in her school for her part in stopping the forced sex culture, as Chuck and Sarah had also supplied footage of the other boys doing similar things to the school. The talk to Molly about why they were all being monitored whenever they were away from home wasn't fun, as they had to explain that there were bad people out there who were still after them, and why she and Emma had to leave their house and move into Castle Carmichael. Sarah and Emma had talked about this previously, and Emma was there to help explain that Jack wasn't actually her father, she had been adopted because her parents had been killed when she was a baby, but she had been rescued and taken away to be left with Emma to look after and raise. When Molly wanted more details Emma looked at Sarah but she shook her head, not wanting to go there until Molly got really upset, so she gave in and stepped up to tell her the whole story, just glossing over how much killing was involved, both when she rescued her and when Reiker came after her ten years ago.
In between their own personal big brother coverage and working, they were trying to track down Riley, the Director and Jasmine to work out what they were doing, and the reasons behind them being here. The tracking them down part was made a little easier by the fact that they'd been monitoring most of the significant criminal organisations ever since BGRU reared its head, especially the ones that BGRU had dealt with, and to get manpower and other resources the trio had to go to them, so they turned up on the radar as soon as they did. Unfortunately that meant that they had to warn the girls not to go out partying and cancel some of the kids' outings because they had confirmation that the newcomer trio were, in fact, there because they were coming after Clan Carmichael, or at least parts of it. One of the outings that they couldn't cancel was the father daughter dance at Molly's high school, because Molly had begged Chuck to take her, she'd never had a father for any important event of her life and her girl friends drooled over Chuck whenever she got dropped off at school by her hottie brother-in-law, so she desperately wanted to show off and be the centre of attention for once. They could give her that, he'd be with her for protection and one of the others would be nearby for back-up, so she'd be safe enough.
The thing that the other side still didn't realise was that most of Carmichael Industries was made up of very good experienced operatives, Sarah, Casey, Chuck, Mary and Carina were among the best there ever was, and Zondra, Josie and Heather weren't too far behind, Stefan and Jeff had both been extremely skilled in spying on people for decades, and Alex and Ellie both had oodles of potential and were being trained by the very best. So for a small organisation of effectively a dozen people (for now), they actually had better resources than most organisations a hundred times their size. That was how they were able to crack the criminal organisations that Riley, the erstwhile Ring Director and Jasmine went to for assistance and get the full details of their plans. The trio hadn't managed to get the location of Castle Carmichael (nor had they apparently gotten the location of the kids' schools, as they weren't staking out the school as Jill had, it looked like Graham had played that card close to his chest) So they were staking out the CI offices to track the CI people, without having much luck as the actual CI team was mostly staying away from the office, and if they did need to go in there they'd swap cars for one of the half dozen that they always had stored in the CI car park, so the watchers would be sitting there waiting for the car that entered to come out, but it would still be in there several hours later.
From what they gleaned from the communications taps and bugs, the trio was looking to grab someone from CI who was significant enough to use as a figurehead, but not dangerous enough to defeat them when they tried the grab, for this reason Chuck, Sarah and Casey were ruled out as they didn't have the army or resources to have a chance of grabbing them without killing them. The prime targets therefore were Mary and Carina, as they were recognisable as significant CI people, but were judged to be a lot "softer" targets than the other three (Chuck, Sarah and Casey couldn't keep the grins off their faces when Mary and Carina heard the recording of that discussion, as they went off in a big way, saying that they'd show them fukn soft targets). They also admitted their real plan when they were trying to negotiate the resources they needed. The point was that it was CI who took their organisation down (like the rest of the significant take downs in the last 10 years), but there were still significant organisation people and resources out there (in hiding for now). So the plan was that they were going to show the others that they could hit back at Carmichael Industries by grabbing a recognisable CI figure and parading them around enough to get enough support to band the remnants together under their control, and then kill them. The plan once they had control of course was to mount a strike to wipe out the rest of CI, so they could settle down and enjoy running their new organisation in peace (they were obviously glossing over the fact that they had no idea how to find the rest of CI, they were probably planning on someone else in the organisation being able to find them once they got control of it).
Now that they knew the plans, and the targets, they sat down to decide how to handle trapping the trio and dealing with their associates. The most obvious approach was use honey pots, set up a number of houses and lead them back to one to take them down, possibly doing the interrogations there. After that, any organisation which was supplying resources to the trio would be taken down and dismantled, but the most important information to them was the location and details of the remnants of BGRU that the trio was trying to get control of. Mary volunteered to be the bait (as Carina was a mother with young children now, one of them being her own grandson), but as none of the trio were present when she was grabbed, she let herself be captured and taken back to them, they knew that the trio needed to keep her alive for their plan to work, so the most she would have to endure would be a bit of torture, if that. Mary was in the game long enough that a bit of torture was nothing she couldn't handle. As soon as they confirmed that the trio was present, the CI team went in with a strike team that the General supplied (one of the ones that they'd used before, as they were the only ones that CI trusted enough to work with), neutralising the mob family that supplied the manpower and resources and leaving the trio to CI to process.
As expected Jasmine had little to offer (she was largely tits and muscle, used to seduce and attack, competent but not part of the inner circle like the other two), so she didn't take long to process, the erstwhile Ring Director and Riley, however, were quite helpful in supplying leads to the BGRU remnants that they were trying to recruit. Chuck had to take over the Ring Director's interrogation as he was starting to succeed in baiting Sarah about her relationship with Shaw, which may have cut the interrogation short and made them miss out on getting all the intel they needed from him, so he stepped in, sent her out of the room and took over. Only then did the Director realise that he had just made his situation worse by trying to bait Sarah into killing him, because through the intersect Chuck knew even more than Sarah about torture techniques, and he wrung the man dry before he finished him. As he'd already stepped in, he conducted Riley's interrogation too, to save Sarah the angst of doing it (she may still be the best in the business, but that didn't mean that doing those things didn't get to her nowadays). Once they had what they needed from the trio they took did a run through of the mob people left alive and Chuck interrogated anyone that he flashed on who was senior enough to have serious information, then they took any and all computer and hardcopy records that they could get their hands on and they left the clean-up to the strike team.
Processing the information that they took away from the operation took them a week or so, they had enough to orchestrate taking down the mob family that had been involved, and track down and deal with a significant portion of what was left of BGRU. That made them busy for the next couple of months, organising the raids on the BGRU facilities and people around the world via the General and the President's team. The operations were still quite dangerous, possibly even more so now as the BGRU remnants now knew what to expect when they were taken (interrogation and death), so they fought harder than they probably would have back when they were smug and arrogant, those who were left now quite literally fought like the cornered rats that they were.
It was the connections in high places who were the biggest problem, they were still coming out of the woodwork as well, and it was a lot more difficult to quietly take a senior government official or other public figure for interrogation and then dispose of them without questions being asked. The "shot resisting arrest" explanation couldn't be used any more, due to the media furor that arose during the primary purge (where thousands were dealt with), so accidents and heart attacks were the primary story now. It also made it difficult to use the tried and true method of ensuring that no-one could recover the body and revive it (blow their brains out), so for public figures the practice was usually to use large amounts of high voltage electricity or acid to burn the brain away (generally after they were dead) the autopsy reports had to be directed or doctored to cover the true facts of the matter, but that was a lot simpler than dealing with public opinion via the media.
In a way there was a silver lining in the clean up of the public figures working for BGRU and other nefarious organisations, the rest of them were now seeing the potential ramifications of their actions, and starting to weigh the whether the benefits (the girls, drugs, money or whatever other pay-offs they were getting for their information and assistance to the dirty organisations) really outweighed the price of their actions, seeing as how many of their compatriots in crime were having accidents, disappearing or were being killed outright when they resisted being arrested (and those left alive knew their type well enough to know that the ones who were taken would never have been brave enough to actually physically resist arrest, so the "resistance" would have been arguing with those who turned up to take them). Anyway, seeing what the true price of the lifestyle that they'd been enjoying was coming to be in the current environment was leading to many of them being "scared straight" and going to the authorities to admit minor infractions that they'd made and spill everything that they knew, in hope that they may live through the new order. So yeah, there was some good (such as it were) that came from the situation, honest (well more honest, anyway) politicians, who'd have thunk it?