When all is lost, it is time to start life anew.
Usual disclaimer, no rights to characters.
Once she had calmed down enough to see Chuck without upsetting him, Sarah took him home to spend the night lost in each other, to try to take some of the pain away.
While Sarah was trying to look after Chuck, Casey found himself in an unaccustomed role, reassuring others that they would all get through the current situation OK. As they had the office to themselves, they closed up and he, Alex and Jeff sat down to discuss what was happening. He started by telling Jeff that, unless he wanted to move out, he could stay at the house with them indefinitely, Alex's argument for the interim solution made sense, so if it worked for all of them, there was no reason to change it, as they all agreed, he went on. With regard to Chuck's implication that he'd be out if he failed in any way on the latest project, that was something that Chuck was stressing about, was now done, and even if there had been something which caused Chuck to go that far, he would have come back and apologised and asked him to return when he calmed down, at that Jeff visibly relaxed, which brought them to the big issue. He couldn't tell them what had them all worked up yet, but he promised that they'd be told when the situation was less volatile and dangerous, it did relate to the issue that Chuck and Sarah had gone off to deal with, and it was the cause of most of Chuck's current state, so all should be back to "normal" in time. Even with the limited information, what he told them took away much of the uncertainty that both Jeff and Alex were feeling, so they could settle down a little then.
The next day, they were all in the office, Casey was trying to get caught up with the new processes, Chuck was less on edge, and while things were still strange, it was workable. Chuck came into Jeff's office early and apologised for the way things had been, he'd been stressing over something that was ultra critical and shouldn't have handled things the way he did. He still seemed stressed and spent a good deal of time on secret video calls that only Sarah or Casey were privy to, but it was more like "old" Chuck than it had been for a while. Sarah was buried in her work, and staying close to Chuck most of the time, she was spending time with Alex, but it wasn't as casual as it had been before. They all hoped that things would settle down relatively quickly, so they could get back to where they were before.
Casey was the one liaising with Ellie on Stephen's test results, and told her on no uncertain terms that she had no recourse, Chuck was too fragile to deal with her as yet and Sarah was too angry.
While awaiting the analysis of the results, Chuck arranged for a good therapist to have sessions with his father to review and assist in his mental stability, both before and after he had discussions with him about the steps that he proposed they should take to give him the best options. The most extreme of these steps were the surgeries he proposed to Stephen. Given that the outlook was good for his mental health with the Intersect largely suppressed, if he was to lead a full life, they had to do what they could to mask or modify the identifying traits that could be used to locate him, he explained to his father the methods he'd used to get evidence that he was where they believed he was. While other organisations may take longer to track him down, the mechanisms were all available, so it wouldn't be safe for him to leave the safe houses without altering those identifying traits. The obvious issue of plastic surgery was part of it, but that wasn't enough, what Chuck was proposing included voice box alterations to change his voice, along with speak therapy, and physical changes and physiotherapy to alter his movement patterns.
Hopefully if all these worked, in time (possibly years down the track), his father could lead a more "normal" life without constantly looking over his shoulder. This was all a lot to deal with, which why Chuck was organising the on-going therapy sessions, and had these discussions with his father face to face where possible. (He used the Nighthawk, it had never been recovered after he "borrowed" it from Castle to try and save Sarah, the weapons systems had been downgraded and modified for local control, and a bike that could travel at airplane speeds let him do the trip to and from the safe houses overnight without drawing anywhere near the attention that planes would.) The choice was his father's, of course, he just presented the rationale as to why he was recommending it without sugar coating anything, there would be a good deal of pain and suffering involved in these procedures, and he respected his father too much to pretend otherwise.
He also told him what was done at the facility that they took him from to make it impossible to definitively determine whether his remains were there or not. The government and other organisations still suspected that Stephen may be out there, but at this time they had no proof, so if they could remove the normal identifiers he may be able to stay free. (Well, one government representative knew, but they lived in hope that she'd honour her word and commitment to keep the secret inside the circle, and she hadn't betrayed their trust in her yet.) To Stephen's credit, he did see the pain and self loathing in Chuck's eyes when he described what was done, and understood what it took for him to do that, they both shed tears the night they discussed what happened during the extraction.
With the information that Chuck gave him, and the prospect if not hope that a more "normal" life could be waiting for him if he made all the changes that Chuck laid out, Stephen agreed with the reasoning and committed to trying that path, understanding that there was no guarantee that it would all work, but he'd been in hiding for over 15 years and the issues that Chuck laid out had repeatedly tripped him up, even when he wasn't being hunted the way he was now, so he was prepared to take the risk, in hope that his son's plan could work.
Stephen talked to Ellie at times, calling Carmichael Industries and getting re-routed to her phone by Casey or Sarah (it hurt him that Chuck and Ellie weren't speaking, but he understood now what had happened and how that affected Chuck), but when he was trying to make casual conversation he slipped up and asked Ellie if she was excited about Sarah's baby, which prompted her to call Sarah. The call did not go well, Ellie was being demanding and petulant, which triggered Sarah's anger about what had happened on the trip to the safe house with Chuck. Ellie found that the fear she'd had of Casey when he was angry with her was nothing compared to the terror that Sarah invoked when she informed her in that cold, dispassionate voice that Ellie had no place or connection in regard to her baby, and that she'd stay away from her family if she was at all sensible. When she hung up the phone, Sarah found that she'd broken all her nails though gripping her desk so hard, she looked up to see Chuck in the doorway watching her, he came over to hold her, and she broke down as soon as she felt his arms around her. After a while, she explained that, as angry as she was for what Ellie had done to him, and she had no doubt that that was justified, she was ashamed of herself as she had done worse than that to him many times over he course of their life together. Chuck just shooshed her as he stroked her hair and kissed her on the head, then kissed her lips as she raised her teary face to him.
Stephen started working on CI projects with Chuck, Sarah and even Jeff sometimes, given that his name obviously couldn't be used, he became Stefan Kowalski. Whenever there was time for lessons, Sarah was teaching him Polish, and forcing him to speak it most of the time, as speaking Polish and acquiring a bit of an accent helped build the identity. Together, they built an identity that was sustainable and over time they settled him into Stefan to the point where he instinctively reacted to that, rather than his old name. The team understood that no mention of their new team member was to be made outside of the CI offices, ever. Jeff and Alex were under the impression that he was located somewhere in Europe, and that was why he always remoted into CI, rather than working directly with them.
His father was upset about having to be cautious of Mary, but the fact that she never made the effort to follow up with them about whether there was any chance that he survived or what happened to him beyond the initial semi-official enquiries appeared to indicate that they'd been right to be concerned, and that she was a CIA agent first, and a wife and mother second. Sarah was angry about that, too, she was as much a spy as Mary, if not as long (obviously), but she wouldn't have given up on the man she loved, ever. She had to concede that the fact that she was angry at everything (except Chuck) could have something to do with the pregnancy and the changes it was wreaking on her body, but she didn't think that that was the whole reason, and neither did Chuck when she discussed it.
Sarah was glad that she had her mother back in her life now, without her she would have had no-one to talk to about the pregnancy and what it was doing to her, now that she and Ellie weren't on speaking terms. Alex was sympathetic, but had never been pregnant, so didn't have any experience with the issues. She could and did talk to Chuck but he didn't know much about what happened during pregnancy, he had the empirical information in the Intersect, and what he gleaned from his extensive research on all aspects of pregnancy (which left him looking worried and frightened quite often), but that didn't really relate to what she was going through, all he could do was try and support her as much as possible, and he did that so well. She did sometimes catch up with Carina, but she was less in touch with the issues than Chuck was. So, having her mother to talk to was the only thing that seemed to keep her sane sometimes.
The family disagreement escalated when Devon called Chuck to tell him that he had to fix things with Ellie, at which point he found that Sarah wasn't the only one who could be terrifying when pushed. Chuck informed his brother in law with small, simple words and a calm, quiet tone of infinite malice that, a, as usual, he didn't know what he was talking about, b, he was interfering in things that were absolutely none of his business, c, if and when he decided to forgive his sister for what she had done and sort things out with her, he would do exactly that, sort it out with HER, d, if he EVER even implied that Chuck should "sort out his wife" again, Chuck would deal with him directly, and in a way that he would not like at all, and e, he should lose Chuck and Sarah's numbers, as if either of them ever heard from him like this again, there would be repercussions. At the end of this he quietly asked whether Devon understood what he'd said to him? At the stuttered affirmative from his brother in law he said "Good, as you are starting to make me angry, and I can assure you that you wouldn't like me when I'm angry." and with that, hung up.
Chuck wasn't happy about how things were going, but he wasn't able to get past his reaction to his sister as yet, and he certainly wasn't in the mood to take crap from his stupid blow-hard brother in law. He had his own life to work out, a business that they were trying to get established, a wonderful wife who was pregnant, and was trying to give his father a new life, while keeping him hidden from just about every government and nefarious organisation in the world, he had quite enough on his plate without worrying about the petty things.
At least Carmichael Industries had plenty of work coming in, a good deal of it contracts from General Beckman. It wasn't charity, in the time they were her team, she knew better than anyone that when she told anyone (even them) that she had "the best people working on it", she was referring to them, and that was largely Chuck. Chuck and his father were the most brilliant men that she, or anyone else, was ever likely to meet, the things that both of them had done were incredible, and couldn't be matched by anyone else the American government could find, and by the records she'd seen, other governments were in the same boat. One of the most amazing things about Chuck, though, was how he brought out he best in others. When Agent Walker and Major Casey were assigned to the Intersect project, they were the best of the best in their fields, but that was largely cleaning up whatever messes that their respective agencies had to deal with. Once exposed to Chuck, they grew and expanded to show their true potential in so many ways, some of the powers that be bemoaned the fact that their elite killers were gone, had been made soft by exposure to this Bartowski individual, but they ignored how much more was accomplished as a result of those changes. If she wanted to be totally honest, he'd had a similar affect on her. She, too, had changed so much from the time that she agreed to the termination order on him to tidy up loose ends. She'd never admit it to anyone, not even Roan, but she regarded this ragtag group as her family in her heart now.
To assist them in meeting their contracts, she fast tracked the clearances of the three people her old team brought into Carmichael Industries. (Though she had a degree of satisfaction in wiping all clearances and accesses for Morgan Grimes as soon as they advised her that all ties between him and CI had been severed, she never liked or trusted that man.) Alexandra McHugh was easy, with an impeccable background and record and all the qualifications to get into any agency she chose, she was a credit to her father, and she had known the girl's father longer than anyone else involved. Jeffrey Barnes was a tad more difficult, the list of misdemeanours , his mother being in prison etc all painted a bad picture, but she was aware of the good work he'd done at Chuck's behest, so she could justify the approval without too much trouble. Stefan Kowalski was another matter, his records and credentials were all impeccable and verified, going back 2 generations, but she knew for a fact they were less than 2 weeks old, Chuck had done a masterful job of inserting and/or amending records across the world, many of them located in the most "un-crackable" systems that existed, and none of what he had done could be traced. He had created an identity which stood up to the highest scrutiny, all in a matter of weeks, so with a smile she approved the requested clearances, actually quite pleased that Bartowski Senior would be joining Bartowski Junior to deal with the world's problems.