Bones 1. Chapter 1

**Disclaimer:** I do not own Bones, any characters, etc.

**A/N:** I know that I already have a multi-chapter fic in the works, but with everything that's been happening on the show lately, my level of angst has hit a dangerous high. So I'm sharing the pain with this new story. Let me know what you think, and how much I should torture Booth for his recent behavior. vehemently wags finger at Booth

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The Admission in the Letter

**Chapter 1**

As Special Agent Seeley Booth walked into the forensics lab of the Jeffersonian, he experienced a nagging feeling of guilt. It had been almost a week since he had even talked to anyone at the lab, let alone visited there. Since the closure of their last case, he had been busy: doing paperwork, assisting on another agent's case, and trying to spend as much time with Hannah as possible given their disparate work schedules. They had started talking about the future and getting married, but Booth knew that was no excuse for slighting his friends. The squints had always been welcoming to Hannah, but in the back of his mind Booth had always felt a little uncomfortable with having Bones and Hannah mingling in the same group of friends. Booth wanted to fix things, though so instead of calling Dr. Brennan about their new case, he had decided to drop into the lab to pick her up and take her to the crime scene.

Glancing up at the forensic platform, Booth felt the first tingle of unease. There were two interns, Dr. Clark Edison and Wendell Bray, examining a skeleton, but Dr. Brennan was not with them. Usually there was only one intern in the lab at a time, and any examination important enough to need two of them would need Bones, right? He glanced towards her office and saw it unlit. He began to walk towards Cam's office to ask her where Bones was, since they did have a case, when he was intercepted by Angela.

"Hi Booth," she said, more coolly than usual, even though her demeanor towards him in the past few months had already changed considerably from two years ago when she used to be happy to see him and referred to him as "Agent Studly."

"Hey, Angela," Booth said, trying to be cheerful despite her obvious antipathy towards his appearance. "Where's Bones? We've got a case!" He tried to infect some of his old enthusiasm into his voice, but Booth and Angela both knew that it was somewhat forced.

Angela didn't immediately answer, looking at him for a minute as if she were studying him. Then she sighed, and motioned for him to follow her to Brennan's office.

When they reached the threshold and Angela flipped on the light, Booth couldn't stop the gasp of surprise from exiting his mouth. He had to look around twice to confirm they were in the right location. Brennan's office was completely different—the usual collection of artifacts, skulls, and haphazardly stacked file folders was gone. There were artifacts on some of the shelves, but they were not the ones Booth had seen many times in his numerous visits to his partner's office. The desk had been moved to a different wall, and only a few file folders were visible in neatly ordered piles.

Booth could only stare at Angela as she stated, "Brennan doesn't work here anymore." Angela's face now betrayed emotions of both sadness and some anger, which Booth felt was directed toward him. Angela reached into her pocket and pulled out an envelope.

"Here. She wrote you a letter," Angela said, her anger apparently growing. "She had asked me to give it to you right after she left, but I decided to wait until you realized she was gone." She glared at him accusingly.

"Gone?" Booth repeated, still in shock. "How could she be gone? I last saw her…" His voice trailed off as he remembered how long it had been since he had seen and talked to his partner.

"Yeah," Angela said, apparently agreeing with Booth's assessment that it had probably been too long to have not contacted someone he called a friend. "This is Clark's office now—I'm sure he wouldn't mind if you sat in here and read the letter. He and Wendell are pretty busy right now." She sighed. "The couch has been moved, but it's still the same one." With another glare in his general direction, Angela left Booth in the doorway clutching the letter.

Mechanically, Booth slowly walked into the office and sat on the couch. His name was written on the outside on the envelope in Bones' familiar handwriting. He lightly traced the name with his fingers, as if he could conjure up its writer by sheer willpower. Then, as he realized that this was apparently his best and only source of information about Brennan, he ripped open the envelope as quickly as possible, letting the envelope drift to the floor as he looked at the neatly written letter. She had taken the time to write it by hand, not typing it as he would have expected. Booth felt another stab of guilt that she had gone to this much trouble for him, who hadn't even called her in almost a week.

Then he began to read the letter, and anyone watching him would have been amazed by the level and variety of emotions that played over his face. However, shock, followed quickly by dejection and misery were the dominant expressions clearly visible on his usually handsome features.

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**A/N: **_Have I gotten your attention? Lucky for you all I wrote the letter first, so I'm posting that next._


	2. Chapter 2

**A/N:** Here's the letter Brennan wrote to Booth. It almost broke _my_ heart to write it, but there was a bit of catharsis in it as well.

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**Chapter 2**

Dear Agent Seeley Booth,

By the time you read this letter, I will most likely already be in Peru. I am sorry that I did not tell you about this in person. Perhaps it is better that you were unable to attend the evening gathering at the Founding Fathers when I made the official announcement to the rest of the team. In this letter, I have attempted to express thoughts and feelings that I might have been unable to articulate in a different medium. I hope that once you have read this letter, you will understand my reasoning, even though I must admit it is not entirely rational. I hope we will be able to regain some of our friendship at a point in the future.

Next I would like to congratulate you on your engagement to Hannah. Since I do not know when you will read this letter, I do not know if the announcement has been made officially, but I was made aware of your intentions a few weeks ago. Please do not be upset with Charlie for telling me. He seemed to believe I already knew, since he was surprised when I asked him why you had been working extra hours to assist him on his surveillance operation. He explained that you needed the extra income to purchase an appropriate ring for Hannah. Although I do not personally subscribe to the need for a material display of affection, I understand that it is meaningful to other people. I applaud you for finding a way to fulfill this need for your girlfriend while also assisting a junior agent on his case—Charlie was very eloquent in his remarks regarding your contribution to the success of his operation.

Booth, I am very happy for you at this development in your relationship with Hannah. I know that you desire to have a wife and family in addition to your career to make your life meaningful and complete. However, although it is an irrational emotion on my part, your happiness in this part of your personal life has resulted in my unhappiness with my personal life. I know that my rejection of your offer of a different kind of relationship many months ago caused you pain. At the time, I did not believe I could give you what you were asking for, what you deserve. One of the main reasons I left the Jeffersonian to go to Maluku was to try to find appropriate perspective on my relationship with you. You had become so important to me, and that was a very frightening thought. You had offered me a romantic relationship, but my romantic relationships have all been unsuccessful. I felt that an attempt at such a relationship with you would be likely to fail, like the others, and then I would also lose your partnership and friendship. The loss of so much was unfathomable.

It is therefore somewhat ironic that by turning you down, and supporting your decision to move on and find someone who could fulfill your romantic needs, our partnership and friendship suffered a serious alteration after all. Although I hate psychology, I have concluded that Sweets was correct when he observed that we had a "surrogate relationship." We did most of the things that romantically involved couples do, spending the majority of our non-working time together. I should have realized that when you found a true romantic partner, you would logically spend that time with her instead of me. I did not understand how important that time was to me, all the dinners and drinks and late-night Thai food, until I discovered it was gone.

I have come to realize that the emotion that I feel towards you must correctly be labeled as love. I was able, with your assistance, to look objectively at my father's actions towards me and determine that he loved me. I have applied a similar set of criteria to my relationship and interactions with you, and although there are limits to the objectivity possible when dealing with emotions, if I am honest with myself and you, I have been in love with you for some time. You are the most important person in my life. If I could give up my life to save yours, I would do so without any hesitation. Even though we have worked so hard together to uphold the law, if I needed to break laws to help you, to save you, I would do so. This ability I have discovered, or perhaps re-discovered, to love someone like this, I have only succeeded in because of you. You taught me how to open my heart, how to demonstrate through actions if not words what true family and friendship really meant. My learning curve is usually steep, however in this instance I was too far behind you to share this revelation with you when it would have meant the most.

But perhaps that was for the best—I believe it was you who told me that 'everything happens for a reason.' Since I was unable to return your love when you offered it to me, you were then later able to find a new love with Hannah. She is able to love you back as you need to be loved, to love you as you deserve. Though I must point out that you were mistaken when you told me that you knew I was the one with whom you wanted to spend 30, 40, or 50 years. Objectively speaking, life is full of moments of change and transformation, and everyone, including me, does make mistakes.

I do not believe my decision to leave the Jeffersonian again to be a mistake, however, I will admit to you that it is a somewhat cowardly action. Once I learned that your relationship with Hannah was going to become permanent, and I realized how I truly felt about you, I knew that I could not remain partners with you and be able to exert sufficient control over my emotions. When my heart was closed, although I was unable to fully experience love, I was shielded from its reverse emotion of pain. It had already been difficult for me to adjust to the decreased level of friendship and interaction with you. However, knowing that I was in love with you and that you did not return that level of emotion, I know I would be unable to complete my work effectively. Our level of "symbiosis," as you once called it, had already begun to suffer as I struggled to come to terms with how I felt about your relationship with Hannah. It is not acceptable to the work that we do to allow my personal feelings to have an impact on the efficacy of our partnership. Therefore, I have decided to join a project in Peru to allow you to work with another forensic anthropologist who will not be impeded by emotional concerns.

The Jeffersonian has hired Dr. Clark Edison to fill my vacated position. He is a fine scientist, and I believe you will find him suitable to continue with the forensic portion of the work we did. He does not have the same desire to assist and observe in the field as I did, so in some ways he may be easier to work with that I was. The Intern Program will also continue, with the interns assisting Dr. Edison with the bone-related examinations of evidence. Dr. Saroyan has agreed to act as an additional mentor towards the interns, although my limited amount of contact possible with the Peru project will enable me to continue to advise the students on their dissertations.

I almost forgot to tell you about the project. You are probably not aware, although I might have mentioned them in passing at some point, that the Incas practiced a form of mummification on some of their departed citizens. It is largely dissimilar from the mummification practiced by the Egyptians, and it has not received the same level of scholarly study. Several specimens were discovered approximately six months ago, and the project organizers requested my assistance on the project. At the time, I did not wish to leave the Jeffersonian and D.C. again. As I described above, I know now that I would not be as effective as previously in continuing to work with you, so it seemed logical at this juncture that I would join the project which can greatly benefit from my experience and expertise.

I wish I could be a better friend, to be there and celebrate the upcoming change in your life. Hopefully once I return from Peru I will be better equipped to support you as you deserve. Please tell Parker about this trip, and that I wish him good luck in his schoolwork. My interaction with your son is another thing about our partnership that I have missed. As you are well aware, he is a very bright and engaging child. Perhaps by the time I return he will have a sibling? I know that you would like more children, and I hope that you will experience all that you desire in your new life.

Your former partner,

Dr. Temperance Brennan

P.S. I did eventually enjoy being called "Bones."

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**A/N: **_So? What do you think? What will/should Booth do next?_


	3. Chapter 3

**A/N:** _Wow, thanks for the response to this! I was betting there were some others out there with angsty feelings, but I didn't expect all the reviews and story alerts. I still haven't completely decided how things are going to unfold, but I am a B&B shipper so good things will happen for them...eventually. And although I did consider it, Booth will NOT be running off to Peru. [Probably not. hehe] (I'm trying to keep things somewhat plausible while still giving us some hope.) _

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Chapter 3

After he finished reading and then re-reading Bones' letter, Booth could only sit on the couch and stare unseeing at the neatly-written pages. His heart had run through so many emotions in such a short time that he felt numb. There was currently only one thought in his mind, repeating incessantly: _Bones is gone_. So he did not hear the footsteps or the voices of the two scientists discussing bone trauma on the latest Limbo case as they approached his partner's former office. Even after Clark had crossed the threshold into his new office, raising his voice slightly, Booth still did not react. Clark and Wendell looked at each other after noticing the strange expression on the face of the FBI agent, and since they did not know what to say or do in the present situation, they quickly exited the office.

"Well, this is something I have not been looking forward to," Wendell said, shaking his head. "How did things get so complicated?" He really liked Dr. Brennan and had always liked Booth, thinking they worked well together, so he had never imagined things would end up this way between the partners.

Clark sighed. With Dr. Brennan in Peru, he had hoped the extraneous interpersonal drama could be kept to a minimum, but even he had known things would be uncomfortable and tense once Booth discovered that Dr. Brennan had left. "I'll go get Dr. Saroyan. Since we apparently have a case, start gathering the appropriate gear and supplies together. Unless the remains are largely fleshed, I think it would help if we both accompanied Agent Booth to the crime scene." He walked to Dr. Saroyan's office as quickly as his level of decorum allowed. Clark was only slightly surprised to find her apparently waiting for him halfway between the two offices.

"I guess Booth has finished reading the letter?" she asked, her voice clearly betraying her concern for her old friend. Cam had felt particularly torn during the last few months. Because of her long-standing friendship with Booth, she felt that her loyalty should lie with him and his wishes. However, in the four-plus years she had worked with Dr. Brennan, Cam had come to rely on Brennan's expertise in the lab in addition to considering her a friend. As an administrator, Cam had fervently wished that Brennan had not felt the need to leave, but as her friend, Cam had supported the decision and agreed to shoulder some of the burden in the lab until Brennan's return.

"Agent Booth did not appear to notice when Wendell and I walked into the office. However, since his eyes did not appear to be focused on anything in particular, I surmise that he has indeed finished reading." Clark paused, not wanting to seem insensitive, but he knew they had a job to do. "Since we apparently have a case, I've instructed Wendell to start getting ready to go to the crime scene. Perhaps you can determine from Booth where that might be?"

"Thanks, Clark. I'll take care of it. Hopefully we'll be leaving in the next 15 minutes." Cam knew that Booth had an almost singular devotion to his work with the FBI, but she also knew he would take the news of Brennan's departure and her reasons for that act very much to heart.

When Cam entered the office that was now Clark's, Booth looked up at her. He opened his mouth as if to say something, but he apparently could not form any words yet since he closed it right away. He tried again, and managed to blurt out, "Bones left us all again?" His voice was shaky, and it seemed to Cam that he was battling between anger and despair.

Cam walked over to the couch and sat down next to her friend, putting an arm around his shoulder. "I'm sorry, Seeley. I wish I had been more forceful when I asked you to join us at the Founding Fathers that night a few weeks ago. Then you would have at least known she was leaving." Cam paused, then added, "Brennan was still planning on telling you some, um, personal things in a letter, but when you couldn't come out with us for a quick drink, we let her persuade us to help her keep her plans a secret from you." Cam herself had felt hurt by Booth's rejection of that offer, but she had since decided that her opinion of Booth's recent actions was the least important of her current worries.

Booth looked up at Cam, understanding the implication in her choice of words. He knew that he had been avoiding all of the squint squad, not just Brennan, and he was glad that Cam seemed to be on his side and apparently wasn't going to ream him out any further for his recent emotional and physical distance. Although part of his brain was telling him to get up and get to the case, another part of his brain was worrying about what trouble Bones was getting into in South America. Yet another part of his brain was trying to ignore the many personal revelations which Bones had described in her letter.

Noticing his focus leaving her again, Cam gently shook his shoulder. "Booth! Don't we have a case? Let's take care of getting the remains brought back here to the Jeffersonian. Once I'm satisfied that Clark and Wendell have things well in hand, you and I can go somewhere and talk." She looked kindly into Booth's face, which was still somewhat pale from the emotional upheaval he had been through that morning.

Some part of Booth's army and agent training reacted to Cam's suggestion. _It's important to take care of the job at hand, to the best of your ability. Worry about the emotional stuff afterward_. "You're right, Cam, of course. At least I get two of the most normal squinterns if I can't have Bones, huh?" he said, trying but failing to make his tone light and jovial, his voice betraying his true emotions when he said the name "Bones."

Cam chose not to point out that Clark was no longer an intern. She did want to allay at least some of Booth's probable fears, though. As they started walking out of the office together, she put her hand on his arm to get his attention. "Dr. Brennan will be returning to the Jeffersonian. She has taken another leave of absence, which will hopefully only last three months." Booth allowed himself to feel somewhat more positive at this news, but he knew that Cam was not telling him everything.

"Hopefully only three months?" he asked, wondering if he really wanted the truth at this point. If Bones had given up her office…

"She told us that she might remain as long as six months, but probably not longer than that. It will largely depend on how the work progresses at the dig." Cam didn't want to give Booth false hope about when Brennan might be returning. Although Cam admitted to herself that a part of her wondered if it would be better or worse—for either partner—for Brennan to stay away for an extended period of time. "Since Clark is taking over responsibility for working with the FBI as the forensic anthropologist, it made sense for him to have Brennan's office near the platform. Most of her belongings have been moved to a vacant office for now. Once we know when she's coming back and in what role, we can decide where she'll end up being located." Cam glanced at Booth again, and she was glad that he did not seem to react to her use of the phrase "in what role." Cam knew Brennan would return to D.C. and the Jeffersonian, but she had her doubts about whether a renewal of the partnership between the anthropologist and the agent would be feasible—or advisable.

Since Booth was still keeping silent, which to Cam was not a good sign since Booth was a talkative person, Cam decided to keep asking him questions about the case to try and keep him focused. Booth began to respond, although his step had none of the forced bravado he had affected when he had entered the lab an hour ago. They had decided that Cam would ride to the crime scene with Booth, while Clark and Wendell went in the Jeffersonian truck with all the equipment and supplies.

Booth was grateful to Cam for keeping the conversation going, and for keeping it strictly work related. He felt a pang with his next thought about how good Bones was about talking about work when one or the other of them was dealing with something uncomfortable. He knew that he would need to spend a long time later processing what Bones had written in that letter, but for now he was glad to have a case to focus on. Unfortunately, since he had spent the last five and half years working on cases with Bones close by his side, he knew that the forensic anthropologist would be in the forefront on his thoughts for the next few hours whether he wanted her there or not.

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**A/N:**_ I had thought the plot would have moved a bit more, but that doesn't always happen. Next chapter we'll be with Brennan on her dig in Peru. :) Let me know what you think. Thanks!_


	4. Chapter 4

**A/N:** _At long last, here is the next chapter! Sorry, RL interferes with creativity sometimes, especially when you work in retail during the Christmas season. But here is a present for all of you who have been wondering about Brennan and her state of mind. Since the Christmas craziness is over at work, I should be able to update more often. _

_Just a reminder: I began this story before "The Doctor in the Photo" aired, so the revelations in that episode did not happen as far as my characters here are concerned._

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_Chapter 4

Dr. Temperance Brennan looked around her tent, finally satisfied with the organization of her belongings. This would be her home for the next few months, three at least, and she tried to make herself as comfortable as possible under the circumstances. She had certainly been on many digs before, but this was her first expedition in years where she planned on spending more than a week or two. In addition to her cot, she had a folding table and chair that served as a desk, where her laptop and files rested, plus a large steamer trunk which served dual functions as clothes dresser and side table. She had placed several framed pictures on the trunk, so that she could have maximum desk space. Brennan often glanced at the pictures while she worked at the table, thinking about her friends and colleagues at the Jeffersonian. She sincerely regretted leaving D.C. while Angela was pregnant, knowing that her friend could use her help and support. However, Angela did have her husband to be with her, and Angela had told Brennan that the anthropologist's peace of mind was more important to Angela than having her friend around to help her baby shop.

Just today, Brennan had added another photograph to the collection, one that Angela had packed for her without her knowledge. It was a candid shot of Brennan and Booth captured at one of the Jeffersonian's Halloween parties. Brennan was, of course, wearing her Wonder Woman outfit, while Booth had gone that year as a pirate. In addition to the usual costume of a billowy white shirt with black pants and boots, he had attached a stuffed parrot to his shoulder. Brennan remembered telling him how anatomically incorrect the parrot was, and Booth had responded by flipping up his eye patch to glare at the bird. That moment, of Booth holding up his eye patch while he and Brennan stared at the silly stuffed animal, was the one that Angela had managed to immortalize on film. It was a simple moment, but one that Brennan had always looked back upon with fondness because it reminded her of how easy it was to be with Booth.

When she had packed her bags to leave, she had deliberately tried not to bring anything that would remind her of Booth. She hadn't brought any photographs that included him, and she had packed the Brainy Smurf and Jasper the Pig figurines away with the items from her office. Angela had obviously raided the boxes stored at the lab, because when Brennan had unpacked her trunk upon reaching camp in Peru, the figurines were carefully packed along with the framed picture of her and Booth. Brennan had allowed herself to cry when she found them, and it had taken almost two weeks before she decided that she wanted to display the photograph. The image reminded her of her friendship with Booth, and that relationship was the one that she hoped to recapture someday once she had moved through her feelings of love. Jasper and Brainy, however, were reminders of their partnership and the strong emotional connection that she shared with Booth, reminders of how far Booth had penetrated into the deeper layers of her life. Since she was trying to distance herself from that aspect of her relationship with her former partner, the smurf and the pig were carefully wrapped and hidden in the bottom of the trunk.

Although she had rarely had trouble immersing herself in her work before, since coming to Peru Brennan admitted to herself that she found her thoughts straying into unwelcome territory more often than she had ever remembered in the past. She was glad that she had decided to travel so far from home, since she was unable to indulge her desires to see or talk to Booth. Since this meant she could also not easily communicate with Angela to discuss the emotional roller coaster she found herself on, she had decided to keep a journal during her time away. Whenever she found herself distracted by her thoughts and feelings, she started writing in it. Brennan had found that by committing her distracting thoughts to paper instead of allowing them to circle aimless around her fertile imagination, she was better able to deal with them.

Another coping mechanism that Brennan had discovered was the ability to talk to the leader of the dig, Dr. Tomas Garcia Marquez. Dr. Marquez had left his prestigious post as Head of Anthropology at the National University of San Marcos in Lima to lead the project. Prior to arriving, Brennan had only known Dr. Marquez by reputation. Upon meeting in person, however, she and the Peruvian scientist had quickly developed a friendship and rapport. Marquez understood how lonely Brennan felt at leaving her friends and family behind. His romantic partner was a professional classical guitarist who traveled throughout South America, concertizing and giving master classes at different universities. Although the pair had been together for five years, they had spent almost half that time living apart and communicating via email and other correspondence. Since Marquez was gay, Brennan enjoyed the lack of sexual tension; tension she had sometimes experienced in working with unmarried male colleagues.

At Marquez's suggestion, Brennan had starting writing daily letters to Angela. Since they did not have email access at the dig site, Marquez had been using this method of corresponding with his partner, Victor Alonso, for several months. Most of the letters were simple, detailing what he had done that day, sharing ordinary thoughts and feelings. Just as Marquez had said, spending time each day writing to Angela helped Brennan feel almost as if she were talking to her friend. Once a week, a messenger came out to the site from Lima, delivering mail to the project and taking mail and reports back to the city. In her first letter to Angela, Brennan explained the dig's weekly mail exchange, and suggested that they each write one letter a day, and then once they started receiving the letters—likely a week's worth at a time—read one letter a day. Using this method, Marquez and Alonso had been able to keep each other informed about the little things of each other's lives, as well as the big events, and they felt it helped their relationship stay strong. Brennan thought about writing letters to Booth, as well, although she didn't feel like she was ready to talk to him quite yet.

Brennan's laptop served as an additional reminder of Booth, since it was issued to her by the F.B.I. The leaders at the Bureau had been unhappy when they heard their best forensic anthropologist would be out of contact for at least three months. Her time away in Maluku had solidified their knowledge that she had made invaluable contributions in solving certain aspects of murder cases. They had therefore determined that an allocation of a laptop with satellite access, in addition to the occasional use of a satellite phone, was an acceptable expenditure to allow Cam and the other scientists to contact her if they needed her opinion. Brennan had used this technology when she and Booth had traveled to other parts of the country on cases in the past, but it was much more expensive to connect from Peru than it was to videoconference from Washington state.

Brennan was interrupted in her musings by the ringing of the satellite phone.

"Brennan here," she said.

"Hi, it's Cam." Dr. Saroyan's voice came through clearly across the connection.

Brennan permitted herself a small smile—it had been less than two weeks and they already needed her help. "What can I do for you, Cam?"

Cam was pleasantly surprised that Brennan sounded somewhat positive. "We've got a case, of course, and Clark would appreciate your thoughts on some bone damage that he believes could be related to cause of death. He and Wendell have been unable to determine what weapon was used. They would like to initiate a videoconference call to show you the X-rays and magnification of the bones."

Although Brennan knew that Cam would not have called unless they needed her for an F.B.I. case, Brennan still felt a twinge at the thought of Booth working in the lab without her. "Just a second, I'll power up the laptop," Brennan said, trying to keep her tone business-like.

"So, is Booth very mad at me?" Brennan asked tentatively.

Cam was not surprised that Brennan had asked about Booth, but she was surprised that Brennan assumed Booth would be feeling anger as opposed to other emotions.

"Well, yes, I think he is a little, but I think his dominant emotion right now is sadness," Cam said, trying to keep her tone as neutral as possible. She didn't want to make Brennan feel bad for leaving, but she also wanted to be honest with her friend.

"Sadness?" Brennan asked, sounding confused.

Cam sighed, wishing the two partners had been more honest with each other.

"He misses you," Cam said sincerely, as Brennan's face appeared on her screen as the satellite link was established.

"Oh," was all Brennan said, but many different emotions flitted across her face that Cam could not quite identify. "Let's get to the case. The satellite usage is expensive."

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**A/N:** _Next chapter we'll get into Booth's head. And (I think) some progress will made in facilitating Brennan's return to D.C. [hint hint]_


	5. Chapter 5

**A/N:** _Here we are, back in the USA with Booth and his thoughts. He's been thinking quite a bit—and he's decided a few things. Hope you like where I'm going. _

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Chapter 5

Booth sank into his chair behind his desk in his office at the Hoover. He had just returned from his meeting with Caroline and Hacker regarding the closure of his latest murder case—the first he had worked without Bones in over five years. Even though the case had not taken any longer than previous cases of similar complexity and circumstances, Booth felt as if the week had dragged by. _A week_, he thought, _it's only been a week since I found out Bones left D.C. Since she left me._ Booth stared at the wall. _You left her first. What did you expect her to do after that?_ Booth stared into his lap, at the hands which were clasping her letter to him. He had carried it in his pocket every day since he'd gotten it. For the few hours of sleep he allowed himself every night, the letter had resided under his pillow. That might have been a problem if he was still sharing a bed with Hannah—but he had been sleeping in Parker's room. Booth had told Hannah that he was still working on Charlie's case, and so he would be coming home in the middle of the night and didn't want to disturb her. Hannah had accepted this explanation so far, but Booth knew that she was suspicious and could sense that there was something else going on. Booth had been working on Charlie's case for the last two months, and there had been only a handful of times that he had come home at odd hours. When he wasn't kept late by the case, he had invented other reasons in his mind to stay away from home: paperwork in his office, target practice at the range, solitaire on his computer…

The truth was that ever since Booth had read his partner's letter and her confession that she had been and still was in love with him, he had been so confused by his own feelings that he didn't feel right sleeping with Hannah. Sharing a bed with Hannah had always led to certain activities, and Booth couldn't even think about those activities without thinking of another woman. Booth knew that wasn't fair to Hannah (or to himself), so he had decided to give himself some time to decide how he was feeling and what he wanted to do with that knowledge. He had admitted to himself that he still had feelings for Bones, but what he needed to determine was whether or not those feelings were stronger and more permanent than the ones he had for Hannah. He had tried to imagine how he would feel if Hannah left him for a few months to go on an assignment, which is essentially what Brennan had done. Booth knew that he would miss his girlfriend, but he had not felt the same sense of near panic he had felt when he knew that Bones was gone. Booth tried to tell himself it was because he was unsure of when Brennan would return, and because things had been left somewhat unsettled between his partner and himself. For the last five and a half years, she had always been there, and now she wasn't.

However, Booth had come to realize over the last few days that he was only fooling himself. Bones had essentially severed their partnership, told him she could no longer be friends with him in the same way that they had before, and that she needed to physically distance herself from him because his current life choices were making her terribly unhappy. At the thought that he was making Bones unhappy, Booth wanted to curl into a ball and cry himself. How had he let things get this way? How had he not noticed that the person he called his best friend was being hurt by his words and actions? He had been so focused on building a relationship with Hannah to cover up the mess he had made with his relationship with Brennan. Instead of working through his feelings for his partner, he had shoved them aside into a secret part of his heart, where he could hide them and hopefully not allow them to hurt him anymore. After reading that letter, the proverbial dam had burst, and his feelings had erupted back to the surface. Booth kept thinking of all the things he loved about Bones, all the things he was going to miss since she was now gone. He realized that he had been missing those things over the past few months, but he had kept himself so busy that he hadn't allowed himself time to think about them. This week, however, he had forced himself to think, to really assess what he wanted from his life and what he believed would make him happy.

A knock on his closed office door interrupted his latest round of introspection. Agent Charlie Burns, the person who had unwittingly set the events in motion that had led to the departure of Dr. Brennan, was waiting outside his office. Booth thought briefly about giving the agent a piece of his mind for revealing secrets which were not his to tell, but then he realized he could ask Charlie about Brennan's reaction to the news. Maybe hearing Charlie's opinion could help Booth solidify his decision, although Booth was already pretty sure he knew what he needed to do.

"Come on in, Charlie," Booth said, trying not to let the weariness he felt seep into his normally business-like tone. He quickly hid Brennan's letter underneath a stack of paperwork.

Charlie looked askance at the senior agent, wondering if his time for reckoning had come. He had heard that Dr. Brennan was no longer at the Jeffersonian, and he had known both Booth and Brennan long enough to have his own hypothesis about what had precipitated her departure.

"I just have a few forms for you to sign, related to my case," he said, his tone neutral. "You know I really appreciated the extra help again this week, but I thought you had already worked enough hours…" Charlie wasn't too surprised to be interrupted by Booth before he could finish his statement.

"Charlie, how did Dr. Brennan react, when you told her why I was working on your case?" Booth asked, his desperate need to known clearly evident in his eyes.

Charlie sighed. He had been half-expecting this question, although he had been personally unaware of whether Brennan had told Booth what the younger agent had told her. Now he had his answer.

"Well, Booth," he began, clearly stalling.

"Just spit it out, Charlie." Booth's impatience was obvious. "I wouldn't have asked if I didn't want to know." Booth paused, then added, "And I would really appreciate the truth, whatever your opinion of that is."

Charlie didn't like to remember that afternoon conversation with Dr. Brennan. He had always liked and respected the anthropologist, even if she was a little odd. The look he had glimpsed in her eyes was not one he would soon forget.

"I thought about telling you before, but…" As Booth continued to glare at him and gesticulate impatiently, Charlie went on: "She tried to smile, tried to seem happy for you. After a few seconds, her face had that look she gets when she's looking at a crime scene—no emotions, just focusing on the job at hand. But before that…I saw pain." Charlie paused, deciding to give his full honest appraisal. "She looked as if I had stolen the puppy out of her arms and then cut one of those arms off." Booth gave Charlie a strange look at his use of hyperbole, but Booth could see that the other man clearly meant what he said. "I've been around you two a fair bit over the years, but I'd never seen that level of emotion from her. Then she seemed to recover from it, thanked me for my time, and left." Charlie felt somewhat relieved after sharing the burden of this experience with Booth.

Booth considered Charlie's words, trying to keep his own emotions from being painfully obvious to the other agent. "Thanks, Charlie. Although part of me wishes you hadn't spilled the beans, maybe you did us all a favor."

Charlie wasn't sure how to interpret this statement, since Booth was currently doing a good impression of Dr. Brennan's ability to mask emotions. Charlie had always hoped that Booth and Brennan would get together someday, but he had given up that hope when Booth had come back from the war with a girlfriend. Booth's statement made Charlie think that either Booth was glad that Dr. Brennan was no longer distracting him, or—as Charlie secretly hoped—Booth had finally realized that his current girlfriend wasn't the right woman for him and would be taking steps to regain the affections of the good doctor. Charlie wordlessly gave Booth the forms to sign, which Booth did, and then Charlie left, closing the door to Booth's office on his way out.

Once he was alone again, Booth allowed himself to succumb to his painful emotions and put his head in his hands. _Bones was in that much pain that Charlie was able to see it? Oh Bones, I'm so sorry…I never wanted to hurt you, never imagined that I was hurting you._ Booth's head snapped up, and he grabbed the letter again. "I should have realized what I was doing," Booth said out loud, to himself. "I will fix this." He heard the determination and resolve in his tone and felt better than he had all week.

He looked around quickly, hoping no one had heard him talking to himself. The normal buzz of the bullpen seemed unchanged, so Booth's moment of clarity had apparently gone unnoticed. He reached into his top right desk drawer and pulled out a small box. The contents of this box represented one potential path of his life. Booth decided he would need to do something really special for Charlie, since the younger agent had, albeit unintentionally, helped Booth realize that the path with Hannah was the wrong one. He needed to find his way back to his true partner.

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**A/N:** _In my mind, once Booth allows himself to realize how much pain he's inflicted on Brennan with what he's been doing, he'll re-evaluate his decisions. I think he's been hiding from his true emotions, allowing only the easy, pleasant ones to remain evident. What he has with Hannah is easy—but it isn't the deep connection he has with Brennan. I'm going to continue to have hope that he'll come to his senses._


	6. Chapter 6

**A/N:** _I know it's been a long time since I've updated this story. This is a long and important chapter, and I wanted to do it right. But the muse didn't want to cooperate. At long last, however, here it is._

_Reminder: I began this story __before__ the revelations of 6.09 (and any subsequent episodes), so my characters are thinking and acting accordingly. (I hope). _

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Chapter 6

As Hannah turned her key in the lock of her current apartment, she wondered what she would find inside. Booth's car was parked in its usual spot, so that meant he was actually home at a decent hour for the first time in almost a week. However, during the few times they had actually been in the same room together during that week, Seeley had been in a strange mood. Up until this week, her boyfriend had been happy-go-lucky most of the time, generally upbeat, not letting the seriousness of his career keep him down. It was one of the many things she loved about him. This week, though, Seeley had been strangely quiet, clearly troubled by something, and Hannah knew that he was avoiding her. She had told him that she didn't mind if he came to bed late—at least he would be there in the morning. But after Booth had declined her invitation for the second day in a row, Hannah had decided that she needed to leave him alone. He obviously had something going on that he wasn't ready to share with her yet.

So she was glad to discover on Friday night that Booth was apparently waiting for her in the apartment. Even though she was looking forward to getting some answers, Hannah couldn't help but be concerned and a little worried about what those answers might be. Seeley had told her that Dr. Brennan had taken a leave of absence from the Jeffersonian, and although he had tried to sound unconcerned about this major change in his professional life, Hannah knew him well enough to sense that there was something he wasn't telling her. She wished she could read him better, and hopefully he would soon be ready to tell her everything. If they were going to get married, Hannah was going to insist on knowing everything Seeley hadn't told her about his relationship with Dr. Brennan.

None of Hannah's imaginings had come close to what she found when she entered the living room. Booth was sitting on the couch, still in his work clothes, so she guessed he had not been home long. Finding Seeley apparently sitting idly on the couch—the TV was off, he wasn't reading some work file—was strange enough. But the oddest thing Hannah noticed was the small, black velvet box sitting on the coffee table. Several disturbing thoughts began to run around in her head. He bought me a ring! But why is it just sitting out on the table like that? Seeley is a traditionalist—this is not how he would propose…so what's going on?

Since Booth hadn't moved or done anything to indicate he realized she was in the apartment, Hannah went around the couch to face him.

"Hi, Seeley," she said, trying to keep her voice light. "I'm glad to see you're home."

Booth finally looked up at her. At the look in his eyes, Hannah involuntarily took a step back. She had never seen him look that serious before. And he did not look at all happy—which she took as a very bad sign since it looked like there was a ring box in front of him.

"Hi, Hannah," he said, his voice a mixture of sadness and resolve. "I've been home for a while, trying to think about what to say. How to say it." Booth paused for a moment, seeming to stare at the small box. He picked up the box and handed it to her, still not saying anything else.

Hannah thought she knew what was inside, although he wasn't asking her the question she thought the box represented. When she opened the lid, she gasped in surprise.

"Seeley! This is the ring that I really…but you said it wasn't within your budget…" She couldn't say anything else as she stared at the beautiful engagement ring.

"I know," Booth said, his voice still heavy with sadness which seemed at odds with the ring he had handed to her. "That's why I started working all those extra hours, helping Charlie with his case… So I could get you what I thought you wanted."

Hannah looked at Booth again—the emotions on his face were not making any sense to her. "You didn't need to do that, Seeley—I would have been happy with whatever ring you chose." Why does he look so sad?

"I know," was all Booth said in response. It looked to Hannah like he wanted to say something else, but when it seemed that he was quiet for too long, Hannah decided it was time to act like the reporter she was and get some answers.

"All right, Seeley. What's wrong? What's going on here? You leave an engagement ring out for me to see, then you hand it to me, but you don't look happy. I've tried to be patient this week, but I think it's time for us to have a serious talk." By now Hannah had put the open ring box down on the coffee table and joined Booth on the couch.

Booth glanced at the ring, sparkling brilliantly against its black velvet backdrop. He took a deep breath, gathering his resolve. "You're right, Hannah. Something is wrong—we do need to talk."

Hannah nodded, trying to look encouraging. She had discovered that being a good reporter wasn't just about asking questions—it was about letting the other person talk and listening to what they said. Sometimes they volunteered information you would never have thought to ask about—or ever expected them to reveal.

"I picked up the ring on Friday, last week. Since you were out of town until Sunday, I figured I'd wait until this weekend to ask—take you out to dinner, the whole nine yards." Booth's tone had become almost emotionless, as if he were telling a story about someone else.

"Then on Monday everything changed. I found out that Bones had gone away again, leaving D.C. for several months at least." Now Hannah had no trouble hearing the sadness in Booth's tone.

Although she wanted to be patient and let him explain, Hannah couldn't help but interject: "So this is about Temperance?"

Booth nodded almost imperceptibly, continuing his story as if he hadn't been interrupted. "We had caught a new case, so I went to the lab to pick her up. I had been avoiding her lately—and I felt bad about that." Hannah could hear the sincerity in his tone. "When I got there, Bones was gone and Angela was waiting for me. She handed me a letter Bones had written to me. Angela told me that she was supposed to give it to me right after Bones had left, over two weeks ago now, but Ange had decided to wait until I came looking for her." Now Booth sounded particularly sad and upset.

Understanding was beginning to dawn in Hannah's mind, but she decided to hold her tongue and see what else Booth would tell her.

"In the letter, Bones explained why she was leaving again. She had run into Charlie a month or so ago and asked him why I was working extra hours. Charlie knows how close we are—or we were," Booth said, clearly upset with himself now, "so he told her that I needed the money to buy a ring for you. Knowing that I was going to propose to you…she had realized that she was in love with me. She didn't think she could do her job properly while watching us get engaged, and plan a wedding... She said she would be too unhappy. So she went to a dig in Peru and arranged things at the lab so that Clark would work with me and Cam would help take care of her interns."

Booth paused, trying not to think too much about what Brennan must have been feeling. He knew all too well the pain of loving someone when you thought that person didn't return the sentiment.

Hannah couldn't resist asking, "So Temperance realized she's in love with you?" Now that Booth had said it, that truth seemed rather obvious to Hannah. Had Brenan really not known that she was in love with Booth? Temperance had always been kind and welcoming to Hannah, but she had also been very protective of Booth—warning Hannah to be sure she was serious about the relationship and not to break Booth's heart.

"Bones didn't ask me for anything—she just wished us well and said she hoped we could be friends again after she returned…which would be after she got over her feelings for me." Booth leaned back against the couch, closing his eyes. He had told Hannah what Bones had said, but he still hadn't gotten to the really difficult part—his reaction to Bones' revelation.

Hannah had been largely quiet so far, but simply knowing that Brennan was in love with him was not an explanation for the non-proposal which had accompanied the engagement ring.

"So Temperance is in love with you," Hannah said again, "and I understand that you're upset about hurting your friend—but what does that have to do with our relationship?" Hannah needed to ask this question, although Booth's current attitude and emotional state seemed to answer the question for him.

Booth didn't answer right away—he seemed to be struggling to find the right words. As Hannah's mind began to put all the pieces together, she started to feel angry. She realized that Seeley must not have been completely honest with her about his relationship with Dr. Brennan.

"You're in love with her, too, aren't you?" Hannah demanded. "That's why you're so upset…that's why you handed the ring to me but didn't actually propose." As Booth merely sat on the couch, not agreeing with her but not denying anything, Hannah's anger grew.

"Don't you think maybe you should have mentioned that at some point, that you were in love with someone else? How long has this been going on? What kind of relationship did you two really have?" Hannah asked, trying not to shout at Booth.

Hannah wished she had asked some of these questions earlier. From the way the partners had talked and acted towards each other, Hannah had suspected there had been something more than friendship for at least one of them at some point. But Seeley's actions towards her, in contrast with how he acted toward his partner, had assured her that his only romantic intentions were toward his girlfriend. And Brennan had seemed happy that Booth had found a girlfriend, and had been very friendly towards Hannah without the jealousy Hannah would have expected if Brennan and Booth had been romantically involved in the past.

"Bones and I were only ever partners and friends," Booth began, wondering if and how he was going to diffuse this situation.

"Really? Just friends?" Hannah asked sarcastically.

"I wanted more. Honestly, I had been in love with her for years. A few months before I left for Afghanistan, I finally told her that I wanted a romantic relationship with her. And she turned me down." Booth sighed.

Hannah was taken aback—she hadn't expected this. "You asked her to be in a relationship with you—and she said no? That doesn't make any sense." Hannah sounded incredulous.

Booth sighed again. "It makes sense if you know Bones. I didn't ask her right, and I pushed her before she was ready."

Now Hannah looked at Booth as if he was crazy. "If it made so much sense, what were you doing with me?" Hannah paused, and a horrible thought came to her, and in her anger she decided to voice it: "Were you just playing around with me until the good doctor decided to say yes?"

Hannah immediately regretted saying that when she saw how hurt Booth looked. "It only made sense much later—especially this week after reading her letter." Booth turned to Hannah and looked deeply into her eyes, hoping she would understand. "I was not 'playing' with you. Bones turned me down and broke my heart. I wanted to move on—I thought I had when I found you."

Hannah nodded. "I didn't mean what I said—I know you would never toy with someone's affections like that." Then Hannah considered the words Booth had used. "I wanted to move on…I thought I had…

"So you tried to move on…but you didn't?" Hannah asked, as her feelings of anger began to fade and were replaced by sadness and hurt.

Booth looked down at his hands, clasped in his lap. When he looked up again, into her eyes, Hannah saw the sadness and regret there, and she knew those feelings were directed towards her. "I moved on as well as I could—you know that I do love you, that I was happy with you…" His voice trailed off as he looked at her, hoping for some confirmation that he hadn't been a complete failure as her boyfriend.

Hannah nodded slowly, not missing the significance of his use of the phrase, 'I was happy with you.' "But you think you could be happier with her?" Hannah couldn't resist asking another question to which she already knew the answer.

Booth tried not to cringe. It was past time to be honest with Hannah. "Hannah, the last thing I want is to hurt you. Although I was still in love with her, I believed that Bones would never want to be with me romantically. And I knew that I wanted a romantic relationship to be truly happy. But knowing now that Bones is in love with me…"

Hannah reached out and put a hand on Booth's arm, trying to give him the courage to say what they both needed to hear.

"It isn't fair to you for us to be together, and especially to think about getting married, when I still have such strong feelings for Bones. She and I never even tried being together as a couple…" He trailed off again, then seemed to gather his strength. "I've had too many regrets in my life, Hannah. I need to try and see what relationship Bones and I could have." Booth took one of Hannah's hands in his. "And you need to be free to find someone who can love you the way you deserve. I tried, but…"

Hannah put a finger on Booth's mouth, stopping him before he could finish his thought—she knew what he meant and that was painful enough.

"You are a good man, Seeley. I'm glad to have known you," Hannah said sincerely.

Booth looked a little chagrined at her compliment. "Well, I haven't had much success as a boyfriend."

Hannah couldn't help smiling wryly. "I would be forced to agree, at least in my case. But hopefully you can make up for that with Temperance?" Even if Hannah wished she was the one Booth really wanted, Hannah knew that Brennan had been completely supportive of Booth's romantic relationship and had never tried to sabotage it. So Hannah hoped that Brennan and Booth could be happy together—it would make something positive come out of her break-up with Seeley.

Booth smiled back sincerely. "You are a fine woman, Hannah. You helped me through a very difficult time—I will always be grateful for that. And not many girlfriends would wish for their ex to have success in his next relationship."

Hannah smiled as brightly as she could, given the circumstances. "Thanks, Seeley."

Hannah and Booth both stared at each other for a moment, wondering what to do next. Hannah broke the silence: "Well, I guess I'll start packing my stuff. And I'll call some of my former editors—I bet one of them would be happy to have me back covering a warzone."

Although Booth thought that Hannah leaving would probably be the best for both of them, his sense of chivalry wouldn't let her suggestion go unchallenged. "You don't need to leave right away," he said.

"It'll just be easiest. I can get a hotel for a few nights—I bet it won't take any longer than that for me to get a new assignment. And it's not like I have that many earthly possessions," Hannah said teasingly. Once she was out of his apartment, then Hannah could allow herself to cry and properly mourn the end of the longest relationship she'd ever had.

"If that's what you want," Booth said, giving her another chance to change her mind.

Hannah nodded, already beginning to get her suitcases out of the closet. "What are you going to do about Temperance? Will you just wait until she gets back from Peru?" Hannah couldn't resist asking—curiosity was an important asset in her line of work.

"I'm not sure yet, although I do have a few ideas," Booth said, trying to keep his tone neutral. His first instinct was to hop on the next plane, but he knew that was impractical. He would need to harness the power of the Squint Squad to even know where Bones was, and Booth thought that one of them in particular had the resources to really help him out. Once Hannah had left, Booth was going to make a long-overdue visit to the Hodgins Estate.

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**A/N:** _I've gotten rid of her again! I decided to make H get angry in this one (I have another story with an amiable, nearly mutual break-up). I sincerely hope things won't get this far on the show, but we all know how the producers like to torment the fans… So now Booth is free to go fight for Brennan. We'll definitely be seeing Dr. B in the next chapter. _


End file.
