Author's Note: After a long wait, here we are with the latest chapter of Second Chances. I had hoped to have it up Sunday night, but I got sidetracked dealing with some personal things. This chapter jumps ahead a few weeks from the previous one, and we are going to the impact that Graham's arrest and the President's new marching orders are going to have on our favorite couple. Just to warn you, this is going to be my longest chapter yet for this story, so you might want to get really comfortable.

Chapter 12

Office of the Director of the National Security Agency

National Security Agency

Fort Meade, MD

October 29, 2007

2130 hours EST (1830 hours PST)

General Beckman looked over the latest mission report from the Intersect project and shook her head in disbelief. While on a cover date with Agent Walker, Chuck Bartowski had flashed on a Chinese agent, Mei-Ling. In the course of the investigation into what the agent was doing, it had been discovered that she was in the United States to try and save her brother from the Chinese Triad. Initially Beckman had been inclined to have the team stand down and not get involved for fear of an international incident. But Bartowski had refused to take that route. Instead, he convinced the Chinese agent to defect, a task made possible because of her own government's unwillingness to help her brother, in exchange for the team's help in rescuing her brother. The team had pulled off the rescue almost flawlessly; Bartowski had even captured Lo Pan, the head of the Los Angeles branch of the Triad!

She shouldn't have been surprised, she told herself. Over the last few weeks, Walker, Casey and Bartowski had successfully completed a number of missions, several of which had major implications. This included the capture of La Ciudad, an international arms dealer virtually every intelligence agency in the free world had been trying to capture for years without success, and the successful recover of a valuable diamond that was to be sold to fund terrorist activity. And all of the success was due, if she were honest with herself, to Chuck Bartowski. Yes he had a vast government database in his head, which helped, but it was his ability to take the information given to him by the Intersect and interpret it in ways that most government analysts wouldn't that was the real advantage. On top of that, she was coming to see that his native intelligence was also a significant factor. Oh she had known he was smart – considering his degree's from Stanford and the reports of his work with Burbank Investigative Services – but she hadn't really realized how smart until now. It made her wonder whether or not he was aware of the game Graham had had Agent Walker pursuing with him. That thought brought her up short.

"If he is aware, he's certainly playing it cool. As far as I can tell, he really does have feelings for Agent Walker." Beckman thought to herself, frowning slightly. She was somewhat out of her element with this operation, as much as she disliked admitting it. Chuck Bartowski was completely unlike any asset or employee she had ever dealt with. Then another thought hit her. "What happens when he finds out?" Taking a deep breath, she came to a decision. It was time to have a talk with Agent Walker.

Bartowski Residence

Echo Park

Los Angeles, CA

October 29, 2007

1830 hours PST (2130 hours EST)

"Hi Sarah." Ellie greeted as her and Devon entered the apartment. Sarah was setting the table while in the kitchen, Chuck was moving around, preparing dinner.

"Hi Ellie." Sarah replied, smiling. "Dinner should be ready in a few minutes."

"Awesome, should give us just enough time to get out of these scrubs." Devon said, before heading down the hall to the bedroom he and Ellie shared. Ellie hesitated for a moment before following, smiling slightly as Sarah walked back into the kitchen. She had to admit, she had been concerned when Chuck had come home all those weeks ago and told her he had met the woman he had been talking to in cyberspace since high school. She had heard too many horror stories of online relationships going bad, some from co-workers, some from patients, and some from the news. Her anxiety was further increased when a few days later Chuck had come home and announced that he had taken a new job with a computer security firm that did work for the government and that he had been recruited by none other than Sarah. While she was happy to see her brother happy and moving on to bigger things, a part of her had been concerned he was moving too fast.

"Luckily I'm a big enough girl to admit when she's wrong." She thought to herself. As the weeks progressed, she was taken with how in tune Chuck and Sarah were with one another. Despite her early misgivings, Sarah was very good for Chuck. And she was quickly becoming a very good friend of Ellie's as well. Shaking herself out of her thoughts, she turned and headed back to the bedroom.

"Hey Sarah, can you hand me the oregano?" Chuck asked, as he stirred the sauce in the pan on the stove. Sarah opened the spice cabinet and located the bottle and handed to him. A second later, her phone beeped. Pulling it from her pocket she looked at the screen.

Agent Walker, we need to talk. Alone. Now. General Beckman.

Sarah's eyebrows rose as she read the message, the walked over to Chuck, showing him the phone.

"What do you think she wants?" he asked in a whisper.

"If I had to guess, she found that piece of paper I conned Graham into signing off on." Sarah responded.

"Are you sure we're ready for this?" Chuck asked. Sarah grinned.

"Don't worry about it. I got this." Sarah said. "Stall with your sister. Casey's at a Ronald Reagan Marathon at the old Markham Theater; I'll take it there. This shouldn't take long."

Apartment of Major John Casey

Echo Park

Los Angeles, CA

October 29, 2007

1835 hours PST (2135 hours EST)

"Good evening, Agent Walker." Beckman said. "I'm sorry to pull you away from your cover date, but I felt this was conversation we better have sooner than later. And in private. I promise it won't take long."

"Yes General." Sarah replied. "Can I ask what this is about?"

"Yes, but first I need to do this." Beckman said, pressing a few buttons on her keyboard. A red light appeared on the corner of the video conference screen. A few seconds later, the sounds of locks engaging both in Casey's apartment and in Beckman's office could be heard. "There. I've utilized my command codes to turn off all the surveillance inside Agent Casey's apartment temporarily. There will be no record of this conversation."

"General? I'm not sure I understand." Sarah said, though she was now certain this was about. "Here we go Walker. Time to take things to the next level." On the screen, Beckman stared at her intently. Then, without saying a word, she stood up, removed her service uniform coat, and with it her rank insignia, and placed it on the back of the chair and sat down.

"Agent Walker…Sarah." Beckman began. "I'm not sure if you recognize the significance of what I just did. It's been something of a unofficial tradition in the military that when an individual of a higher rank or who exercises authority over another member removes their rank insignia, that it is to be taken to mean that the conversation or interaction that is about to occur is not between subordinate and superior, but between peers. Mainly it is usually only used between NCOs and enlisted, but given the nature of this conversation, I wanted to make the gesture. Do you understand?"

"Yes General." Sarah replied.

"Sarah, for the next few minutes, I think it's best if you addressed me as Diane." Beckman said. Sarah's eyebrows rose in interested.

"Yes Gen…Diane." She said.

"Good. Just be clear. This conversation is between two women and agents. And completely off the record. I will be completely honest and open with you, and I expect the same in return. No harm will come to your career based on what you say in the next few minutes, as long as you are COMPLETELY honest with me." Beckman said. "The reason for this meeting is to discuss how to proceed forward with regards to Mr. Bartowski and yourself."

"I'm not sure I understand." Sarah said, trying to resist the urge to smile. She had been right.

"When this operation started, Chuck Bartowski was an asset, nothing more. As you know, there is standard procedures for dealing with assets. At the time, Graham and I agreed that having you pose as Mr. Bartowski's girlfriend made sense. I was also aware, based on your record that you never engaged in the traditional honey-pot traps that other female agents often use. So imagine my surprise when I found a note in Graham's files after they were turned over to me and I found a memo from Graham in the Intersect project folder detailing that he had given you permission to pursue what can only be described as a long-term modified honey-pot trap. Specifically, that in order ensure control over the asset, you had been given permission, and apparently accepted the permission, of engaging in the necessary activities to convince the asset you were falling in love with him and pursuing a long-term relationship." Beckman said. "Now, to say this would be out of character for you is an understatement. Likewise, from what I know of Graham, for him to specifically document such an approach on paper. He was clearly trying to protect you if somewhere down the road someone started asking questions. Am I close?"

"Yes." Sarah replied. "I requested he put something in my file. I was afraid that someone would decide I was going off the reservation."

"Someone like me, perhaps?" Beckman asked, then waved her hand silencing Sarah before she could speak again. "You are of course, correct. While he was classified as an asset, had I thought you were engaging an a long-term, real relationship with him, I would have had to put a stop to it – especially since I was left out of the loop as to what was going on by Graham.

Unfortunately, now we have a new problem. As you are aware, the President had issued new directives to the intelligence agencies in general, and to the Intersect project specifically, in wake of the discovery of Graham's crimes and activities. Chief among them is that in the case of Mr. Bartowski, he is explicitly NOT to be considered an asset. He is now officially a government employee, classified as a Field Analyst-in-Training. As such, you and Major Casey are now his partners and protective detail. So the rules and methods related to assets are no longer in play. This leads to the problem I spoke of earlier. If the President finds out we are running a honey pot trap on Mr. Bartowski, we will all be lucky if we are able to find employment scraping ice off of igloos in Alaska. I've also come to appreciate that Mr. Bartowski is in fact, a very intelligent and perceptive person. If he were to discover what you were doing, it could be equally as disastrous. My people here are telling me that it is very likely that the ability of the Intersect to present viable data is tied to the mental and emotional state of the person housing it."

"I agree, Diane." Sarah said. "I've noticed when Chuck is over stressed or upset, the flashes aren't as effective."

"Good. So we are left with the question of what to do." Beckman said. "As I said, if the President was to find out that this has all been a modified honey-pot trap, and eventually he will, we are all going to be in trouble. That is, assuming it HAS all been an act, Sarah."

"Holy shit!" Sarah thought, trying to stay calm. "Looks like I didn't give her enough credit."

"I'm not sure what you mean, Diane." Sarah said.

"Contrary to what you, or Major Casey, or a lot of others may think, Sarah, I'm not stupid. I may be a Rear Echelon Motherfucker (REMF) now, but I was also a damned good agent in my day. I can put 2+2 together, and read between the lines as good as the next agent. Like I said, what Graham's files indicated was VERY out of character for you. Which leads me to one of three conclusions.

Conclusion One – there is something more about Mr. Bartowski's abilities that you and Graham aren't telling me; something that makes him so valuable that you are willing to cross a line that you drew very early and clearly in your career. One that Graham had always respected, until now.

Conclusion Two – that Graham had something on you, something so dangerous that he was able to force you to cross your well-drawn line.

Or Conclusion Three – that for whatever reason, you decided to throw away your training and career and pursue a real relationship with Mr. Bartowski. And that this piece of paper was either Graham's conscious attempt to shield you, which I find unlikely. Or you either blackmailed or conned him into giving it to you." Beckman said. "If it's one or two, then I need to know what you and Graham haven't told me. Immediately. And we need to start planning a strategy to deescalate the relationship and let it fizzle. I'd prefer not to reassign you to another mission and have to bring another agent in, but I will if there's no other option. If its number 3, then I still want to know everything. Due to the President's instructions regarding Mr. Bartowski, a real relationship with him would not be automatically be disallowed, as relationships between agents, or agents and other employees, are not against regulations. Provided everyone involved can remain professional when needed. So, which is it Sarah?"

Sarah's mind raced as she examined all the angles and consequences. She had been expected an inquiry about Graham's memo. She hadn't expected Beckman to figure out that it might be there as smoke screen to protect her from the consequences of a real relationship with Chuck. She was also surprised that Beckman had not complained or shown reluctance over the President's recent directions.

"Before I answer that, Diane, I need to ask you a question." Sarah said, making her decision.

"And that is?"

"I know you couldn't have been thrilled with the President's new directives. From a purely operational standpoint, they make our job more difficult. And as someone who's been in your position for as long as you have, it couldn't have been easy having to move away from what you know. So why are you not more reluctant about all this?" Sarah asked.

"Three reasons. First, I'm a soldier, Sarah. And when a soldier is given a lawful order by her Commander-in-Chief, she obeys. Whether or not I agree with it." Beckman replied, stiffly, then softened. "Second, because after reading everything that that bastard Graham has done, I've come to see the President's point. We have over the years as a community gotten to use to skirting the lines of legality and ethical behavior. And that allowed Graham to get away with what he did for so long. And at times we've chosen to do things based on what was most convenient rather than what was best for the nation and our people. Third, as I've watch your team these past few weeks, I've come to the conclusion that Chuck Bartowski, as unorthodox a spy as he is, is the sole reason for the success we've had. And I'm not just talking about the Intersect. He is certainly intelligent and resourceful. And his unconventional way of looking at things has given us victories we never would have had. And he's done it all with little to no formal training. He's also taken two of the intelligence communities' best agents, who normally work alone, even prefer to do that, and help mold them into a team. Does that answer your question?"

"Yes." Sarah said, taking a deep breath before continuing. "You're right. About all of it. Initially I had intended to pursue my normal method of stringing the asset along with the vague promise of sex, but that went out the window pretty quickly. First because from his file and after engaging him in person that first day, it was obvious that it wouldn't work. Second, he was unlike any many I had ever met. By the time our "date" on that second day was over, I was taken with him. I wanted to get to know him – not as an asset, but as a man. So I concocted the long-term relationship honey-pot trap modification and sold it to Graham. I knew someone might start asking questions, and I needed a get out of jail free card."

"I see." Beckman said. "And now that you've had a few weeks to get to know him? Have your feelings changed?"

"Yes, Diane. They have. I'm falling in love with him. There's no other way to put it." Sarah said, looking away from the screen for a moment before returning it and standing up straighter. "But I have kept my focus and remained professional when necessary. It has not interfered with my ability to do my job. In fact, I think it's helped."

"Does he know?"

"How I feel about him? Yes. About what I asked Graham to do? And why I had to ask? Yes. He knows everything, Diane." Sarah replied. "You're right, he's very smart and perceptive. Even before I told him about Graham, he had guessed that there could be problems if he and I got too close."

"And Major Casey?"

"I have not told him the truth. But Major Casey isn't stupid either, nor is he as ignorant of people's emotions as he pretends to be. I would be very surprised if he doesn't suspect something is up, even if he doesn't know quite what it is."

Beckman remained quiet for a few moments, processing what she had just been told. She had in truth suspected that this might be the case; it was the only thing that made sense in her mind. Contrary to what she had told Sarah, she didn't think the first two options she had presented were very likely. Plus, she was also a woman. A woman who had also been in love and still was if she were honest with herself. After what seemed like an eternity to Sarah, but was really only another one or two minutes, she spoke.

"Very well. Given Mr. Bartowski's new status per the President's direction, your team's phenomenal success rate over the last few weeks, and the fact that you've behaved professionally when and where appropriately, I see no reason to open the can of worms that would follow by transferring you out of Los Angeles. I would ask you to be discreet, at least for now, since Mr. Bartowski is still technically a trainee. If you can do that, I can look the other way for a few more weeks until he is official." Beckman said. "However, there are some conditions that I will insist upon. First, I expect that your relationship will not interfere with your team's job. The minute I get the sense that it's impacting the ability of the team to do what it needs to, I will step in and end it. Two, Major Casey is to be brought in on EVERYTHING. I'll handle that. He is going to be my eyes and ears on this. And third, we are going to have to have another agent assigned to the team."

"What? Why?" Sarah asked, surprised. She hadn't foreseen this possibility.

"Because Sarah, as much as I believe that you will be able to continue operating in a professional manner, the fact remains that you are now emotionally compromised. There may come a time where that becomes a liability. If that happens, you'll need more than just Major Casey to back you up. And if it becomes too much of a distraction, having the extra agent already in place with mean less of an impact if I have to transfer you." Beckman said. "I don't anticipate either situation, to be honest. You're too good an agent. But I'd be derelict in my duty if I didn't cover the contingency."

"Who?" Sarah asked.

"I haven't decided that yet. I have two or three possibilities in mind. I'm going wait until I speak with Major Casey before coming to that decision." Beckman said. "Rest assured, picking someone who can easily integrate into the team and get along with everyone is something I will be looking at very carefully. Now get back to your dinner."

Bartowski Residence

Echo Park

Los Angeles, CA

October 29, 2007

1935 hours PST

"That was an awesome meal, guys." Devon said as he picked up his and Ellie's plate to carry them into the kitchen. "Just what I needed after a long day in the operating room."

"Thanks Devon." Chuck said. "I know it's not up to Ellie's standard of cooking yet."

"Chuck, it was really good. I'm impressed. It won't be long before I think I'll have to turn all the cooking over to you, little brother." Ellie said, teasingly. Chuck blushed slightly, the usual reaction he had to praise from his older sister.

"Thanks Ellie. But it wasn't all me. Sarah helped." Chuck said, leaning over and giving Sarah a peck on the cheek. "She's pretty handy in the kitchen."

Now it was Sarah's turn to blush slightly. One of the things she had concentrated on over the last few years awaiting her chance to come to Los Angeles and see Chuck was to improve her cooking skills. In the other timeline she had enjoyed these meals the four of them would have together, but always felt a little sad and guilty that she couldn't contribute much to the actual preparation. So she had vowed to change that this time around. She didn't think she was up to Chuck's level yet and definitely not Ellie's but at lease she wasn't completely out of her league this time around.

"Thank you for saying that sweetheart." She said to Chuck. "But the truth is I didn't do much. Chuck did most of the work."

"Well, whoever was responsible, good job." Ellie said. "So movie night?" Sarah and Chuck exchanged glances and nodded.

"Sure. It's been a while since I've been able to just sit and enjoy a good film." Sarah said, then looked at Chuck. "Just no science fiction or superhero movies this time." Ellie laughed.

"Not to worry. I've got plenty of non-geek movies to choose from." Ellie said.

"Nerd! How many times do I have to tell you Ellie, its Nerd, not Geek!" Chuck said indignantly while Sarah, Devon and Ellie devolved into laughter.

Apartment of Major John Casey

Echo Park

Los Angeles, CA

October 29, 2007

2200 hours PST (1900 hours EST)

"I'm sorry to pull you away from your movie marathon, John." Beckman said to her favorite subordinate and protégé. "But something important has come up."

"No problem General." Casey responded. "Do I need to get Bartowski and Walker as well?"

"No. While this conversation does relate to them, there's no need to have them present. I've already spoken with Agent Walker." Beckman said. She paused, reinitiating the same security procedures she had used with Walker.

"General?"

"John, I'm going to tell you the same thing I told Walker earlier. This conversation is strictly off the record." Beckman said. She then proceeded to fill Casey in on her conversation with Walker. When she had finished, Casey grunted in amusement.

"Looks like I was right." He thought to himself, smugly.

"You don't seem very surprised, John." Beckman stated.

"No ma'am. I was getting some vibes. Nothing I could prove, though."

"I see. And since you couldn't prove anything, you decided not to bring it to my attention?" Beckman asked. "Or was it that you felt you owed Agent Walker for Prague?"

"You knew about that?" Casey asked, surprised. Beckman grinned slightly.

"As I told Agent Walker, I may be a REMF now, but that doesn't mean I've lost my skills." Beckman said, sternly.

"Yes ma'am."

"Relax, John." Beckman said. "You did the right thing, especially in light of the President's new orders. So don't worry about it. I trust that your judgement was well thought out and correct. Going forward, however, I need to know that you'll report any significant impacts their relationship has on operations, particularly the negative ones. And by that I mean issues that cause tension or team dis-cohesion. Other than that, I don't want to know, as long as they can keep things professional at work."

"Permission to speak freely?" Casey asked.

"Granted."

"General, why aren't you more upset about all this? Even with the President's orders, this goes against long established rules and protocol." Casey asked. Beckman sighed, suddenly looking older than she was.

"Because I've spent the last few weeks looking over all the files on what Graham was up to." Beckman replied. "And I've had to do a lot of self-reflection and soul-searching because of it. As much as I want to dismiss Graham as an aberration, I can't. Oh, don't get me wrong, he's certainly an outlier – I don't think there is a current US intelligence director or agent that went so far off the reservation as he did. But it happens more than I care to admit. And he was able to get away with it for so long because we as a community got to use to putting expediency over methods; myself included. Mr. Bartowski's situation is a perfect example. We had all the data ahead of time that should have told us that Mr. Bartowski was not involved with Larkin. That he was an innocent caught up through no fault of his own. Yet look how Graham and I reacted. We initially proceeded as though he was like any other asset that came into the path of the CIA and NSA. We didn't care that he was an American citizen, even. I basically ordered you to capture him and through him into a bunker, without trial. Is it any wonder someone like Graham was able to get away with the things he did? Well no more. Between the President's orders and my own self-reflection, I'm determined to make things right."

"And this other agent you want to assign?" Casey asked.

"I have three candidates in mind. One is definitely my preference." Beckman said, then grinned. "Though I'm not sure how you'll feel about it."

Outside Sarah Walker's Car Outside of Bartowski Residence

Echo Park

Los Angeles, CA

October 29, 2007

2300 hours PST

"So she's really okay with us?" Chuck asked, looking at Sarah in disbelief. The two of them had just walked out of Chuck's apartment and made their way to where Sarah's car was parked on the street.

"I don't know if I would go so far to say as we don't have to worry at all." Sarah said. "But right now she seems to be willing to look the other way. Part of that is the President's new directives. As for the rest? I'm not sure. It could be that Graham's arrest and the revelations about everything he's been up to over the years really did cause her to have a moment of real introspection and she really has had a change in view on how things should proceed. Or it could be she's being a good spy and telling us what we want to hear and trying to give us the rope to hang ourselves.

If it's the first one, then we still need to be careful, Chuck. Just because she's more willing to do things differently and let us have a relationship doesn't mean that she would hesitate to step in and yank us apart if our relationship caused issues operationally. So as much as I want to celebrate this victory by dragging you back to my hotel room and ravishing you until dawn, I think we need to stay on course and continue to take things slow. If for no other reason than to show her we are being reasonable and responsible about this. Plus, I don't think either of us is quite ready for that step yet."

"Yeah, you're right." Chuck replied. "As much as my hormones are screaming at me right now, I don't think it'd be a good idea yet either. The issues with Beckman and the government aside, I don't want to screw this, us, up by moving too fast. But what if it's the second possibility with Beckman?" Sarah stepped closer to Chuck and pulled him into an embrace and kissed him. A moment later she whispered in his ear.

"Don't worry, I've still got a few tricks up my sleeve. I think I can get her to back off if necessary. In fact, if who I suspect may be on her list of agents to bring into the team as a fourth is correct, it will actually help our situation. There's only a handful of agents that I think she would trust to work with us. Luckily for us, most of them either owe me big time or I've established a pretty good relationship with them over the years – though I'm sure Beckman is quite aware of it. I've always been very careful to not let the CIA or NSA know everything about me; I always had a feeling that someday it would be necessary to catch them by surprise. But I won't lie. It's possible that all my efforts might fail. In that case, we need to be prepared to run, Chuck. We'd need to go completely off-grid and disappear. I already have a basic plan in place if we need it, and some resources and allies to help us. I know it's a lot to ask, but it might be the only way to stay together and keep you out of bunker." Sarah said.

"What about Devon and Ellie?" Chuck asked. "And Morgan?" Sarah rested her head on his shoulder and sighed.

"I think we could probably take Devon and Ellie with us, if they were willing." Sarah said. "But I don't know about Morgan. I'm sorry Chuck, I know he's your best friend. And I like him a lot too. But the more people involved in this, the harder it would be. Besides, he won't be in danger from the government if we run, unlike Devon and Ellie. Being family, they'd be the primary leverage the government would look to use against you. I promise I'll do everything I can to make sure he's safe before we leave though."

"Ok." Chuck said. "I kind of figured that would be the case, and I get it. And thank you for including Ellie and Devon in your plan. I don't think I could live with leaving them. And for trying to keep Morgan safe, even if he can't go with us. But you're wrong about one thing, Sarah. Morgan may be my best male friend, but he's not my best friend overall. That's you. And you're not just my best friend. You're so much more. I know we just agree to take things slow, but I need to tell you. I'm no longer just falling for you, Sarah. I'm head over heels in love with you." Sarah pulled her head up and looked at Chuck.

"Oh, Chuck." She said, tears of happiness forming in her eyes. "I love you too." Then she leaned forward and captured his lips again, kissing him with more passion then they had yet engaged in. He quickly returned the kiss. After a few moments, the need for oxygen forced them to pull apart. "I better go before my resolve completely implodes. I'll see you tomorrow." With that, she turned and got into her car before speeding off. Chuck watched her drive off for a moment, then turned and walked back to his apartment.

Undisclosed Location

October 29, 2007

2300 hours

A beep alerted the occupant of the small room to the computer on the desk. The figure got up from the table on the other side of the room and walked over to the computer. After entering a password, the screen flashed and Microsoft Outlook appeared, with a new message in the inbox. A mouse click later and the e-mail content was displayed.

"Interesting." The figure murmured. "Very interesting."