Just because you're paranoid, it doesn't mean that they're NOT out to get you.
Usual disclaimer for the land of Litigation, no rights to any characters...
Chuck and Stefan spent the next two weeks working flat out to get through the umpteen layers of encryption on the files that they'd pilfered from the BGRU sites. As soon as they had them in a usable state they passed them onto the others for analysis. While they were excited about cracking the files, seeing what they were getting out of them was making their world get darker by the day (by the hour in some cases), they were getting a wealth of information about BGRU, and it was far worse than they'd ever imagined, or feared. The Puppet Master had connections at all levels throughout the world's governments, and he appeared to be in a position to take control of a significant proportion of them when he made his move, he'd obviously been planning this up for decades, probably most of his adult life as many of them appeared to go back 30-40 years. On top of that, the names of the people in the organisation that they extracted from the records were the worst adversaries they'd ever come up against, including the previous Ring director, Shaw of course, and a host of others.
One thing that they did confirm from the files was that the Puppet Master was based in the same facility as the Intersect project (which made sense, as they expected that having access to the Intersect databases was what he was waiting on to make his move), so they pulled Mary and Zondra out of Chicago and brought them home. It was just too dangerous for them to be in Chicago when Graham and others who could identify them were there. They left the strike team that Casey and the General had arranged to support Mary and Carina in place, so that they'd have resources available if and when they were in a position to take the facility. Mary and Zondra were the last to find out about Langston Graham, as there here had been no way of securing the communications enough, and if the had worst happened and they'd been taken, the fact that they'd ascertained his identity didn't get out. They were as shocked as anyone was when they were told, but could understand why they hadn't been told before that.
Chuck was making daily trips to DC in the MiniStar (they'd acquired the ΒΌ scale single seat flight prototype of the SonicStar by virtue of basically buying the company, and luckily the smaller plane could operate out of a small local airstrip) to hand deliver each day's findings to the General (and, in some instances, the President). The General and the President were organising with a dozen trusted allies around the world (most of whom were also heads of state) to monitor and arrange to take down the key BGRU points of presence, so Chuck was delivering the intel to them so that they could pass the relevant sections on to the people it impacted the most.
As well as analysing the files they extracted, they were still searching the net for any other information or indicators about BGRU. It was no faster than it had been earlier (the Puppet Master controlled his people well), but they were managing to accumulate a little more each day. By now they had a relatively comprehensive map of who was located in which BGRU facility, and who the key members that they HAD to get when they took them, so all the key BGRU people were subjects of individual searches, to flag every sighting and mention of them. After a bit over four months, Clan Carmichael, the General and the President's team agreed that they had nearly all the information that they could get without making a move on BGRU, that they had all the key BGRU people targeted and tracked, and that they had trusted teams available to take any key BGRU facilities and associates. Chuck and Sarah (and the others) didn't want to go back into the field but agreed that this was too critical, they just couldn't sit this one out, so Clan Carmichael was going to be taking a significant role in the raid on the Chicago Intersect facility take out their Intersect project, and the Puppet Master. What no-one outside the family knew was that there was an ultra secure safe room buried well below the bunkers under Castle Carmichael, so Ellie, Clara, Kathleen, Stefan, Jeff, Charlie, Emma, Molly, Yvonne, Zack, Jaqueline and Piotr were all safely ensconced in there while everyone else (even Heather) took part in the raid on the Intersect facility. Stefan and Jeff would be providing technical support from the safe room, but all of the family's non-combatants were safely locked away in there. The safe room was designed to handle a direct hit from a reasonable sized nuclear bomb, so they would be safe in there.
When they were gearing up for the assault on the Intersect facility, they decided to share the Thumpers etc with the team that they'd be taking from Castle Carmichael, needless to say their eyes lit up (they were candy to guys like that), but they were going to need every bit of help they could get if they wanted to get through this alive. While none of them discussed it, they didn't really expect all of them to live through it, so they looked around their family with sad eyes, wondering who would come out the other side of this. Of course, Carina and Zondra being who they were, they both turned to Sarah to say "Fuck it, there's a chance that we may never have another shot at this", and walked up to Chuck to drag him into mad, passionate kisses that were just short of sex, thanking the stunned Chuck afterwards and telling Sarah that they could see what she saw in him now, it was the only lightening of the mood that they got as Casey and Heather pissed themselves laughing, Mary and Alex grinned and Sarah smiled as she went to comfort Chuck after he was "assaulted".
They were in contact with Stefan and Jeff all the way to Chicago and they blasted straight into the facility when they got there, the other strike team were nearby, waiting, and they breached at the same time. The teams split up, some taking out the communications facilities, some taking the security facilities, some focusing on the Intersect project and Chuck and Sarah's team heading for the Puppet Master. Mary was the only family member that went with Chuck and Sarah, Casey took Alex and Carina with him to take the Intersect project and Zondra, Josie and Heather were on the other teams. As expected, Graham had kept the cream of the security for himself, so they had to go through Mr Colt and Hugo Panzer and their teams to get to him, but given the magnitude of what they were facing, Chuck had given up on non-lethal solutions this time, his main priority was for his family to survive this, and that meant he had to deal with Graham and the BGRU on their terms. Colt, Panzer and the rest in the way of getting to Graham were taken out in a hail of inhumanly fast and accurate shots, and when they found that the door to Graham's office was pretty much a vault door, Chuck called everyone back, pulled the Thumper from where it was slung across his back and blew it in. Chuck and Sarah were the first through the door, taking out all the security people he had in the room (except for the ones who had been obliterated by the door when it blew in), and tranqued Graham before he could react.
Once that was done, they had the team remove all the bodies and vacate the room while they secured Graham to a chair in the middle of the room and waited for him to regain consciousness. When Graham came to, he looked around at Chuck, Sarah and Mary, and smirked, thinking that he knew how this would go, given Chuck's moral position on death and torture. He was therefore rather surprised when Sarah stepped up to him, drove a spike into his shoulder and asked whether she had his attention, while Chuck looked on without turning a hair. He looked at her in shock without saying a word, so she did it again, and that time he frantically pleaded with her to stop. Now that they'd set the tone for the interrogation, Mary turned to guard the door while Sarah began getting information out of Graham, the strike teams hadn't let them down yet but they couldn't really trust anyone outside of the family at that point.
In the space of the next couple of hours, Sarah extracted the plan that Graham had been working on for the past 40 odd years, and Graham progressively lost fingers and accumulated other injuries. At point he asked Chuck how he could be letting this happen, and Chuck looked him in the eye and said that sometimes, evil must be met with evil for the greater good, before turning away. Sarah leaned in and quietly asked Graham if he remembered all the things he'd put her through and made her do for the greater good?
Apparently Graham had always been ambitious (well, a megalomaniac, actually), from the time that he joined the agency, he'd been scheming to get to "his rightful position". He'd killed or otherwise removed anyone in his way, and the way he gloated about how he'd framed, blackmailed or otherwise destroyed the various unfortunate individuals (and their families) that he considered an impediment to what was his rightful due as he chronicled his rise to power made his listeners start thinking that the ones who were killed outright may have been the lucky ones (even Mary looked a trifle green, and she'd been the right hand of one of the world's biggest psychopaths for over 20 years until that persona was suppressed and Hartley was released to take over again). Even though two of the three listeners effectively had eidetic memories, they recorded the interrogation as they would not be releasing this monster afterwards.
Graham was quite prepared, if not proud, to describe how his plans had developed over the past 40 years, and what he'd done to bring them to fruition, the sneer as he looked at the three of them occasionally made them wonder what he was up to, but they presumed (correctly) that it would come out. If Graham was to be believed, he'd been instrumental in pushing the CIA's Intersect project forward, and at the very least he knew all the details, right back to the start, even down to the fact that a certain promising young agent was assigned to protect and manage Stephen Bartowski when he was engaged to work on the project (Chuck caught his mother's eye and asked a question with a look, not missing her look of concern as she nodded infinitesimally, Sarah shared a concerned look of her own with him over that response). Graham talked about the testing programs that were rolled out in universities and high schools to determine the best potential Intersect hosts (Chuck turned to quickly stare at him with that, as they'd never heard of testing being done anywhere else but at universities), and how anyone with promisingly high results was flagged and monitored (Sarah was looking away at that point, but Chuck noted with dread the brief look that Graham cast at her when he said that). Given that Graham had no loyalty to anyone but himself, he made no bones about naming the multitudes of lost souls (and just plain monsters) that he'd recruited and turned over the past 40 odd years to do his bidding, and quite a few of those names were at this time people of considerable power and influence, when those houses were cleaned, there would be considerable upheaval around the world in the seats of power. He had spent over 40 years, quite literally planning to seize world dominance, and the scariest part of that was that this time, he would have had a good chance of doing so if they hadn't stopped him.
He finally got up to the point about 5-6 years before when Chuck was supposed to be "replaced" by the new Intersect. Since Bryce sent the Intersect to Chuck (under orders from him), his plans had received a few setbacks, he was supposed to get total control of the Intersect project so he could progress things in the best direction (both Chuck and Sarah looked at him when he said that, uneasy about his tone), but some political hacks had convinced the powers that be that it needed to be a joint CIA/NSA project with both sides keeping an eye on each other, so that bitch Beckman became the major thorn in his side, always getting in the way, questioning or interfering with his directives or reporting what he was doing, and the people backing her had considerable political power, so the only way to bring his plans to fruition was to disappear. He boastfully detailed the process he'd followed and Sarah had been exactly right, except that she'd missed the fact the he also engineered the explosion to take out all of the CIA's Intersect prospects and infrastructure, effectively hamstringing the CIA's Intersect aspirations, and leaving Chuck as the only Intersect resource in existence. The best part was that all it took was a two bit actor that as close to his height, build and appearance (plastic surgery made appearance good enough to fool just about anyone, and he had been cultivating the abrupt, authoritarian personality for decades to keep people at a distance, ensuring that they didn't look him in the eye or attempt to engage him in any way).
Sarah asked why he'd risk getting Chuck terminated if the plan was to ensure that Chuck was indispensable, and he spat back that Beckman had given the order to her robot too early, and almost got him killed, the order wasn't supposed to be given until after the new Intersect was operational, and of course then it would have been cancelled before anyone was dispatched to carry it out. Chuck was supposed to be put on hold and under protection until the other plans for him panned out, but of course Beckman and her robot screwed all that up, too. Sarah asked what the other plans were but he clammed up, until he lost another finger joint to get him talking.
Graham glared at her with a look of utter hatred, then sneered as he told her that she was meant to get attached to Chuck and manage him the way that Frost was induced to manage his father. Both Sarah and Mary stared at Graham in shock, while Chuck began to succumb to a rare fit of rage as he heard that two of the three most important women in his life, his wife and his birth mother (Ellie was more of an actual mother) had been groomed and conditioned to be, basically, concubines to himself and his father by the CIA. He started to advance on Graham but Sarah recovered quickly enough to stop him, telling him quietly that she needed to get this information out of Graham while they had a chance, looking into his eyes from less than a foot away until she saw the rage recede and sanity return. She kissed him and asked if he was OK as she held her palm to his chest. He nodded shakily and she kissed him again before turning back to Graham.
It took a bit more inducement to get Graham to pick up the story again as he thought he'd won that point, but Sarah got him talking again. When he said that that much of her training and conditioning had been to groom her for her role with Bartowski, it was Sarah that had to be held back, as she said that she was doing her job, but she fell in love with Chuck. Graham sneered at that, gloating that she, or more to the point she and Bartowski, had been following the scripts that were laid out for them for the last 15 years, turning his head to Mary to add that SHE had been following her scripts for 35 years now. Turning back to Sarah he gave her a malicious smirk as he told her she'd been selected as a result of the tests that they slipped into the high school aptitude testing process, and when they'd discovered her father's occupation it was easy to set it up for him to be arrested so that he had a hook to get her under his control.
Her appearance was a disaster then, but at least she had the basics that they could mould into something that they could work with. Then they had to train her from scratch to know how to behave in the right circumstances, and THAT took a lot of work, he added with a oily smirk (Chuck took a step forward again, but his mother took his arm and he managed to get himself under control). Graham conceded that Sarah had surprised them with her physical, martial arts and firearms capabilities, they never expected that someone like her, who was primarily selected for her intellect and the mental capabilities that she was tested for would be much good for anything else, so that was a bonus, they weren't too surprised by her ability to soak up languages or pretty much anything else, as that WAS part of what she was selected for. Once she was trained properly in ALL areas (this added with another oily smirk), her conditioning process was started to ensure that she'd do whatever she was told to do, and she was put into circumstances where only his intervention could save her, so she'd be suitably grateful and obedient. They ran through that process for 5-6 years to make sure she would do what she was supposed to. The later phases were primarily to build links that they planned to use down the track, like Larkin, though he hadn't minded playing with her after they'd managed to mould her into a worthwhile sex toy with all their efforts. The Budapest situation almost went astray though, she was supposed to get in trouble and be rescued (and therefore suitably grateful), but Reiker had gotten greedy and thought he could get a good pay day out of it, if that had ruined all his work Reiker would have taken a long time to die, but as she'd came out that in a good state of mind to be set up with Bartowski, he'd let Reiker live, and ordered Larkin to initiate the Intersect transfer to Bartowski and start the next act of the show.
At this point he turned his head to sneer at Chuck, saying that he'd been a lot easier to mould into what they wanted, what he was bred for. All three heads came up to stare at him with murder in their eyes, so he focused on Mary, saying that for someone with an IQ like her's, she was clueless, she'd done everything that she'd been told to (aside from actually falling love with Stephen Bartowski), she delivered the first generation of the super spy breeding program and then went off to babysit Volkoff for 20 years when poor Hartley's persona encoding went wrong. Roarke had screwed up the changes he was supposed to make to the Volkoff encoding, but that was OK, even with his screw up the end affect was what they wanted, to keep her out of the way. Her laughed, saying that she'd been so eager to please when she was selected for the plum assignment of looking after their technical wizard, Stephen Bartowski, believing that she was selected because of her performance and dedication to duty. He conceded that her performance was right up there, far and away better than any other female agent in her day, but she was primarily selected because of her intelligence and physical capabilities, and the fact that she was fairly attractive and the right type to appeal to Bartowski (adding "senior" as he looked at Chuck) helped as well. He did say that the fact that they (laughing) fell in love probably helped with the prime aim, which was to breed superior spies, to try and meld Bartowski's brain with a woman who was almost as intelligent and who had the physical capabilities to counter his amazing lack of them. They let her off the hook and chose not to punish her, but rather let her have the babies when it was found that she'd gotten pregnant. Of course, they couldn't have her there playing Mommy as that would have gotten in the way of the children being moulded into what they wanted them to be, so they manufactured the scenario where they needed to insert an artificial weapons dealer into the European arena. It wasn't too hard to convince Bartowski to create a mechanism to temporarily to implant an artificial personality into a subject, and as Hartley Winterbottom trusted that it would be safe as long as as his friend did it, he volunteered to be the subject. It was easy to get Roarke to make the requested changes to the program, if he baulked at the money offered they would have sent the pictures to the mob boss of Roarke and his under-aged daughter. Of course Roarke screwed up the job he was given, but the end result was the same, "Volkoff" was there to stay, and Frost went in to keep an eye on him until Bartowski could find a way to fix the problem. Once she was over there, it was a simple matter to leak enough details about her to "Volkoff" to make her do a deal to stay there, in hope that her family wasn't discovered.
Bartowski senior was a problem though, he ended up falling apart because he was lovesick (Graham looked over at Chuck with disdain as he said it was obviously a family trait) and disappeared as well a few years later, that fitted into the breeding scheme, but hampered the Intersect project, as Perseus and Roarke weren't good enough to finish the development without him. The CIA and NSA were throwing all the resources it could into tracking him down, but the reason that they wanted his genes (that incredible brain) worked against them here, as he was always several steps ahead of them. In the meantime, however, they inserted people into the younger Bartowskis' lives to keep pushing them in the right direction. The girl wasn't malleable enough to keep her heading in the desired direction, she went into medicine and it was pretty obvious that they wouldn't be able to get her down the agent path, pity, she had the intellect and physical capabilities, at least she was still viable as breeding material.
Once he'd got the boy into Stanford with the right scholarship, he'd used suitable recruits via the CIA and Fulcrum to keep him in line and push him in the required direction, Larkin was set up as his room mate to always keep him in sight and keep him away from anything that may help him see behind the curtains. When they re-tested him at Stanford, he was almost off the charts in most areas, above his father and with vast amounts of retention capability. He didn't go down the athletic path, but they saw enough signs to know that he did have the requisite physical capabilities, if largely latent at that point. Roberts was set up as his girlfriend to keep him from making any solid associations with other women, they had considered her as a possible breeding partner, but while she had a good intellect and impressive physical capabilities, she wasn't good enough to match up to Bartowski's potential, so they continued to with the plan to groom Walker for that role, another benefit with Walker was that she was almost up to Bartowski's retention levels (96% against 98%), so their progeny should have higher capabilities than either of them. (Sarah and Chuck looked at each other with that statement, and Chuck said that they were told that Bryce had had the next highest score. Graham snorted, saying that they'd suppressed her scores so she wouldn't attract attention and boosted Larkin's so he would look like a more viable candidate.)
Graham looked around the room, he knew he wasn't likely to get out of there, but he reasoned that at least he'd get the story about his brilliant plans and how he'd managed to make most of them come to fruition out to the world, or at least the intelligence community, that could be his legacy. And besides, this way he could torture and hopefully destroy these people who had interfered with his plans.
After the interruption Graham continued, telling how Larkin had set Bartowski up to get him kicked out and left his scripted speech about saving him where it could be found in the future. Roberts was instructed to sleep with Larkin, get caught and "break up" with Bartowski. That wasn't a hard sell for either Larkin or Roberts as they'd both screw anything that would stay still long enough. So they extracted Bartowski from his safe environment and got him out of the CIA's sight, so they could mould him properly. The problem was that he was such a pathetic sop that he fell apart because his "girlfriend" screwed around and left him. So they spent the next few years monitoring him and giving him the occasional nudge to try to get him headed in the right direction, while they groomed Walker to be the perfect rescue from that life (Sarah desperately wanted to rip the tongue out of Grahams' mouth at this point, but they needed to know what he'd set in play, all the more so now that he'd set them up as a super agent breeding plan, so she said and did nothing, but buried her face in Chuck's chest when he put his arm around her, they were standing behind Graham and out of his line of sight unless he turned his head completely around, so he was just staring at Mary and goading her as he talked).
After the Budapest incident, Walker was primed to engage so he ordered Larkin to "steal" the Intersect and blow up the facility, then send the Intersect files to Bartowski to get them loaded into him. Casey getting there in time to shoot Larkin was a hitch in the process, as they needed him for some elements down the track, so he had the body recovered ASAP and had the Ring revival process commenced at the earliest opportunity. He was aware that Larkin probably wouldn't be 100%, but all he needed was for him to play the role a few times, and luckily he'd always been shallow and vapid, so with any luck he'd be good enough to pull it off. He laughed when he referred to Walker's "pathetic attempt to redeem herself" after the previous failures, but Bartowski was hooked straight away and things were looking like they were on track until those stupid politicians saddled him with the bitch and her robot.
Once the setup was in place, another hitch appeared when she fell for Bartowski, to prevent Beckman getting enough evidence to remove her he tried sending a few distractions her way (which showed that he was right, of course, to push the issue to have Larkin revived), and even then Beckman almost managed to get rid of her with the 49B, but Beckman's political connections would have held up his plans way too long, so he arranged to "die" so he could have a free hand to run with them. Of course, the fact that Bartowski loaded the Intersect 2.0 was a surprise, he'd underestimated the lovesick puppy dog, just like he did his father, which meant that a lot of the plans had to be modified, but the pay-off was the fact that Bartowski senior was back now, and they could get the Intersect project back on track. To keep his options open, he had Larkin revived again, but it was obvious that this time he couldn't pull off the act of being "Bryce" any more, but there were some benefits in having a rabid dog prowling around frightening people, it distracted them and made it easier to get things done when you didn't want others noticing.
Without any direct control of the situation, the plans around Walker and Bartowski started to bog down so he'd set up impeccable credentials for Daniel Shaw and arranged for him to be sent in to control the team. The fact that he'd had Shaw's wife killed to keep him under control years ago (not noticing the looks of disgust he was getting when he mused that he may not have done that if she was better in bed) backfired on him as he was unhinged, and when he saw that Walker was falling apart about the situation with Bartowski, he played her insecurities to get her into bed, which was really screwing up the plans. He had been amused when their acting on their feelings for each other were what it took to get his plans back on track, but never let it be said that he'd look a gift horse in the mouth, and it saved him the effort of having to kill Shaw for interfering with his plans, but like Larkin, the long view said that Shaw may be needed so be had his body recovered from the river and revived, once it was found.
So with the breeding pair heading in the right direction, he'd been working on his organisations and associations, he'd basically been pushing Fulcrum and the Ring in the direction he wanted for years, and using them to get things done, but Walker and Bartowski (and the robot, he grudgingly admitted) made a surprisingly effective team once Bartowski started realising his potential in an attempt to impress Walker. They took down Fulcrum, the Ring and Volkoff Industries so fast that he'd hardly had time to extract the key resources and people he needed, and in some instances he didn't have enough time. He poured his resources into the "new" Ring and started moving on his overall plans, but then the old team were back and taking down his new organisation. This time he lost most of his resources, and had to call in just about every favour to get re-started. The good thing was that, though he may have very few resources to kick-start his organisation, he did have dirt on a plethora of people who couldn't afford for him to talk, so money, equipment and facilities flowed his way, and he set up the substitution process to get the ex Ring, Fulcrum and just plain dirty agents, and the other manpower and skillsets they needed.
He'd kept an eye on Larkin in case he needed him, and was rather surprised when Roberts ran into him at the organisation where he worked (as she was working as an escort there). Graham had ordered Larkin to engage Roberts in case she could be useful, so when Larkin took her back to her place to screw her and reported that she had a son and that the father was Bartowski, Graham realised that Roberts could most definitely be useful. After a few hour's coaching Larkin appeared to be just "normal" enough to pitch the scam to Roberts that she deserved better than having to sleep with half a dozen marks a day to be able to support herself and the boy. Anyway, it worked and Roberts went in to her her "share" of the money. Of course she was captured immediately and sent back to the supermax, but within a week she was dead in a "fight" with another prisoner, and her son had a new "Mommy" who was part of the Carmichael operation.
As he'd finished his story, he craned around to look at Sarah, asking how she'd done it? She sighed and schooled her expression before turning to face him and asked "Did what?" When he said, tracked them down, organised the take down and executed it without him suspecting a thing, she smiled up at Chuck as she said "Ask my husband, that was his doing." Graham looked at her in disbelief and then shrugged (as well as he could while tied hand and foot to the chair), saying that at least he'd had the last laugh, because by now the person that he'd planted in their little organisation would have taken their children away to prepare them to embrace their destiny. He'd been right about the breeding prospects of Roberts and her, the child that Roberts had produced was exceptional, but he wasn't even close to the ones that she'd produced for them. The second generation of his breeding program had indeed produced the super spies he wanted. Chuck surreptitiously pulled out his phone, unlocked it and brought up the video feed from the safe room, and the kids were all there with the family, fine, he showed Sarah the video to prove that they were safe just before Graham sealed his fate, saying that his main regret was that he wouldn't have the chance to train her daughters, as he'd promised himself that he'd do that personally this time. Sarah's face instantly froze into a mask of homicidal rage as she spun with a snarl, pulling a pair of pistols and emptying them into his body, shredding it. When both weapons were empty she kept them trained on him, and kept pulling the triggers until Chuck gently took them off her and pulled her into his arms. She jerked when he emptied the tub mag left on one pistol into Graham's head, so that there wasn't much left of it. She looked up at him with a question and he grimly whispered the he was making sure that THAT evil could never come back. Sarah nodded without a word as she she held onto him as if her life depended on it.
Chuck looked at his mother and she nodded, stepping out to call Stefan and ensure that they didn't open the safe room until the family was back, organised someone to pick up Bella, checked on the rest of the family, finding with relief that they all came through with no more than minor flesh wounds, and calling the General to report the outcome of the operation (after telling her that Josie was fine).