Author's Note: Thank you for all of the encouraging reviews, messages, follows and favorites for the first chapter - they are really appreciated and I am delighted so many of you are enjoying the story already!

For the purposes of this series, I'm writing the missing scenes in order of the episode's production codes rather than the order in which they aired. A few plot lines are out of sync with the latter order (such as Booth taking Bones to Wong Foos or when he receives his Jeffersonian pass after he'd already used it in the previous episode?), so it made more sense for me to try and build this story in the way the first season was actually filmed.

Once again, thanks to writingherhope for the beta and for agrainne24 for listening to me ramble on about Bones instead of Stargate for a while. ;)

Chapter 2: A Boy in the Tree

Angela studied her best friend as she sat at her desk and stared blankly at her computer screen. She'd noticed Brennan had been quiet ever since her return from the Venezuelan Embassy with Booth, but whether it was due to the sensitive nature of Nestor Olivos' death or something else, the artist wasn't sure. She cast a quick glance around the lab and seeing everyone else was busy, headed for Brennan's office.

"Sweetie?"

She knocked gently on the door and was surprised when her friend jumped. Usually, Brennan was hyper-aware of her surroundings but on this occasion, she'd been lost in her thoughts and in those few seconds she had been unable to hide her emotions – nor the tell-tale glisten in her eyes. Without hesitation, Angela stepped into the office and closed the door.

"Talk to me," she said quietly as she took a seat in front of the desk and waited patiently, giving the scientist the time she needed to work through her thoughts. When the silence started to linger for too long, however, Angela leaned forward and repeated her request and after a moment of hesitation, Brennan met her concerned gaze then quickly looked away.

"Booth said I'm bad with people."

Angela sighed. A part of her hoped she knew what Booth may have meant by his words, so she was prepared to give him the benefit of the doubt for the time-being and – until she could ask him personally – she'd assume that Brennan had simply misinterpreted their conversation. She decided it was a likely possibility, given her friend's straightforward way of looking at things, compared to Booth's more instinctually-driven methods.

She had tried to give Booth an insight into his new partner a few weeks earlier during the Cleo Eller case. She'd even issued a gentle warning that there was more to Brennan that meets the eye and while Booth had seemed to take her advice on board and the pair had agreed to continue working together, Angela realized that it would take him a while to understand just how complex and deep and thoughtful Brennan actually was. Just like it would take Brennan a while to realize that Booth could help her learn more when it came to social etiquette.

Angela stifled another sigh. It wasn't completely Brennan's fault. Over the past year, she'd come to know her friend well enough to know that part of her awkwardness and uncertainty with social gatherings was a result of her time in the foster system. In her opinion, the fact that her friend had essentially been on her own since she was fifteen: having to look out for herself and having no-one to help her or even wanting to help her, no doubt influenced how she now dealt with people and society as a whole.

For a long time, no-one had shown Brennan what it meant to have a meaningful relationship – even if it was just a friendship; or what it felt like to have someone care about you and worry about you. She hadn't been given any reason, any proof, that she could trust someone other than herself.

So, when their paths crossed just over a year ago and they'd started to become friends, Angela had taken it upon herself to be there for Brennan in any way she could. In addition to being there for advice, she had tried her best to introduce her to more societal settings and to a life outside of her work, but Angela knew she still had a long way to go and she'd be damned if Booth succeeded in hindering their progress.

She was just about to offer a word of encouragement when she saw a flash of hurt in her friend's eyes.

"He said I shouldn't be offended by the fact and I know I am not the most comfortable in situations that involve heightened emotions," Brennan admitted, "but it doesn't mean I don't care, Angela. Booth says he's good at reading people; he should know that I care."

Suddenly, the artist was angry that someone could misunderstand and hurt her best friend – unintentionally or otherwise – and she silently vowed to have a word with Booth the next time she saw him.

"I know you care, sweetie," she finally said as she grabbed her friend's hand and squeezed, "I know."

It had been over an hour since her talk with Brennan and while Angela had work to do, she decided it could wait until she finished another – and in her opinion – more pressing task.

She held her clipboard close to her chest, just in case Goodman or someone else walked by and asked what she was doing, but in all honesty she didn't really care. She was worried about her friend – and subsequently trying not to be angry with Booth. She knew he was due to arrive for an update on the case, so she continued to slowly pace back and forth near the entrance doors to the lab so she could confront him the moment he appeared.

She didn't plan to cause a scene but she did want to know what, exactly, the two of them had talked about when Booth told his partner that she was 'bad with people' and until she had Studly's side of the story, Angela had simply tried to comfort her best friend.

When it came to friendships and social interactions, Angela knew Brennan missed the nuances and subtleties; the general 'rules' that went alongside those relationships. Even her physical relationships with men were more about satisfying biological urges as opposed to a deeper bond based on love or any real emotion.

But it didn't mean that Brennan didn't care. She was, inherently, a scientist and this permeated itself into every aspect of her life. Facts were her constant; her truth; the one thing she had been able to rely on over the years. People, they've come and gone in her life, but the facts? They've always been there. Yet Angela had made it a priority to try to break through the scientist's oft-brusque demeanour and open her mind – and heart – to the possibility that not everything in the world is bad. That there are some people in life that you could rely on and trust to be there when you needed them. And she knew her friend had listened and tried to take her life lessons on board, but there were times when Brennan continued to insist that she didn't need anyone to share her life with, nor did she care what others thought of her as a result. Yet Angela couldn't help but notice that this was the second time in a matter of weeks that Brennan had questioned her lack of people skills – and it was purely because of something Booth had said.

Angela felt conflicted. She wanted to be mad at Booth for his behaviour but she knew he still didn't know Brennan the way she deserved to be known. She was also curious as to why Booth's opinion was the one that suddenly started to hold significance for her friend. Angela had been around enough people and been involved in enough relationships to suspect there were deeper feelings lurking beneath the surface for the partners.

Ever since the agent had arrived back into the lives of the Jeffersonian team, Angela had made a point of watching him and Brennan interact; the way they spoke and acted around each other, and on more than one occasion she'd caught him sneaking glances at his partner when he thought no-one else was looking. She also knew her friend viewed Booth as easy on the eyes. When thrown in with their almost constant bickering – science versus people, facts versus instinct – it all added to an intense unresolved sexual tension and Angela wanted a front row seat to see how the partnership developed, particularly given the contents of Brennan's new book, Bred in the Bone.

Angela chuckled quietly. She has no doubts that Kathy and Andy were really Brennan and Booth on some subconscious level – even though her friend strenuously denied the resemblances that everyone else could see between themselves and the characters – and she wondered if the agent had read the book and, if he had, what his thoughts were on the characters and their intermingled work and personal relationships.

With a small smile, she decided she would ask him some time. For now, she would simply keep a close eye on the pair so she could confirm her own suspicions that they liked each other, but before she could ponder the thought any further, the doors to the lab opened and in walked the person she wanted to see – Special Agent Seeley Booth. He'd only taken a few steps when Angela spoke.

"Did you tell Brennan that she was bad with people?"

Booth stopped and sighed as he turned to face her. "She told you about that?"

Her eyes widened at his immediate admission and she scoffed in disbelief. "So, it's true?"

"What?" he asked defensively. "In case you hadn't noticed, Bones isn't exactly the life and soul of the party around here, is she?"

"You hurt her feelings."

He pulled a face. "She has feelings?"

"That's uncalled for Booth – and you know it," accused Angela.

"Yeah," he winced, and she knew he felt guilty over the comment. He sighed again and gestured around the Medico-Legal Lab. "Got somewhere we can talk? Squint free?"

He followed Angela into her office and as she closed the door behind him, he hovered uncertainly until she gestured to the couch. He shook his head, then shoved his hands into his pockets and started to pace the room.

"Aren't you going to say something?" he asked a few moments later as he glanced at the artist.

She gave him a quick onceover and smirked. "Nice tie."

"Thanks," he said distractedly. "Bones said –" He glanced down at his tie and then back at Angela who was suddenly looking at him with renewed interest.

"Bones said what?"

"Nothing." Booth cleared his throat and resumed walking. He absolutely refused to reveal the reason he'd started to wear colored and patterned ties was because of a passing comment his partner had made over a year ago. "Can we discuss something else?"

"You're the one who asked to talk, Studly," she shrugged. "So, get talking."

"Okay, fine," he grumbled. "Yes, I told Bones she's bad with people – but she is," he defended. "She doesn't want to relate to the law enforcement agencies we work with; she can't identify with the families who've lost their loved one –"

He kept pacing as he talked and Angela studied him closely "– and for all of her intelligence, Bones doesn't seem to be able to grasp how to talk to people in these situations. She refers to them as victims to their face," he continued, almost in disgust. "But they aren't. Cleo Eller was someone's daughter; Nestor Olivos is somebody's son. They're people – they should be treated with respect."

At his final words, Angela straightened. "What do you think Brennan is trying to do?"

Booth spun on his heel to face her. "Excuse me?"

"You don't think she's being respectful?"

"I never said that," he countered, lifting an index finger and pointing in her direction.

"It was implied."

He opened his mouth to argue but then realized that Angela was right. He stared at her for a moment as he decided on what to say next when she sighed.

"Look, I understand, okay? I've spent enough time with Brennan to know she doesn't have a natural ability when it comes to social settings, but –"

"But?"

He watched her closely as she glanced at her closed office door and then sat down. "She's my best friend and fiercely protective of her personal life," she said carefully. "I need to know I can trust you, Booth; that this conversation stays between us."

He immediately stopped pacing and instead perched on the edge of the desk. "Yeah," he said. "You can trust me."

Angela nodded as if to convince herself more than anyone else. "Okay. Remember a few weeks ago, when I told you that Brennan cares about her work and how she works tirelessly to give the missing a face and a name?"

Booth nodded. "Yeah, I remember. She gives families closure," he repeated solemnly as he thought back to his previous chat with the artist.

"So, you also remember that she's been in the system?"

He nodded again.

"It's not something she talks about – even with me – but I know she didn't have the best experience."

At this, Booth's eyebrows rose and Angela shrugged. "The only reason I know as much as I do is because we had one too many drinks one night; otherwise, I don't know if she'd have said anything."

He pursed his lips and gestured for her to continue but his thoughts were now on his partner and her experience as a foster child. He'd worked for the FBI long enough to know exactly how bad some of the homes could be and he felt an inexplicable surge of anger towards anyone that may have mistreated his partner when she was younger. Before he could go too far down a road he wasn't sure he wanted to travel however, Angela's voice cut through his thoughts.

"Brennan was fifteen when she had to go into the system, but within those few years she was constantly moved between homes, schools and towns. No-one wanted her," she said, her voice wavering. "No-one knew how to deal with her – or seemed to want to learn – because of her intelligence and her personality. She was punished because of who she was, Booth," Angela continued more strongly as she met his eye, "and, in turn, this taught her not to trust anyone because anyone she did have in her life only betrayed her or let her down. She acts the way she does today because she can't remember a time when she didn't have to be this way. She learned to build up these walls in order to protect herself so she doesn't keep getting hurt."

Suddenly, Booth felt guilty.

"You're partners," Angela continued softly as she got to her feet and took a couple of steps towards him, "and I know you need to be able to trust her, but talking to the families of victims and being part of interrogations? It's all new to Brennan – just like our science is new to you."

His jaw twitched as he listened to her explanation and he sighed. "What do you suggest I do?"

"Help her to understand," she said as if it was the most obvious answer in the world.

"It's not like Bones is going to listen to anything I have to say right now," he argued. "She doesn't even like me."

"Oh, Brennan likes you," Angela smiled and Booth involuntarily straightened.

"Yeah?"

"She wouldn't give you the time of day otherwise."

"Oh," he said, deflating slightly for a reason he wasn't sure why. "Right."

A beat of silence passed before Angela spoke again. "She needs to know that she can trust you."

"Bones can trust me," he fired back.

"Really?" Angela asked dubiously. "People have treated Brennan badly for almost half of her life – and you told her that she was bad with people."

"I didn't mean –" He ran a hand through his hair in frustration. "I just –"

"I know, Booth," she conceded, "and I'm not saying you and Brennan can't have disagreements. Hell," she smirked, "it wouldn't be the two of you if you didn't, but don't use it to attack her integrity or character. It'll make you no better than the others who've gone before and made her believe she isn't good enough."

The veiled accusation stung but Booth couldn't find it in himself to disagree because he knew Angela was – once again – right when it came to his partner. At the time, he'd been frustrated with Bones and he hadn't thought about how his words could affect the woman by his side. A woman he still, despite thinking he did, didn't really know at all.

She'd hurt his feelings when she'd suggested she was smarter than him, and in many ways she was right, but he was street smart, which should also have counted for something and instead of them being able to talk the issues out, he'd thrown her words back in her face, not realizing that just as he had misinterpreted her argument, she could also have misinterpreted his.

He sighed. Booth prided himself on treating people, particularly women, with respect yet he'd been anything but respectful to Bones earlier. He briefly closed his eyes and pinched the bridge of his nose before he glanced at Angela.

"You're right," he admitted.

Usually, Booth had no problem apologizing if he was in the wrong but he seemed to be spending a hell of a lot of his time apologizing to his partner in the few short weeks they'd started working together again and he really was trying not to make it a habit. He also suspected that 'I'm sorry' would only cut it so many times with the forensic anthropologist before she told him where he could shove his apologies.

He pursed his lips and decided he needed to let Bones know that he wasn't like the others. That he would be there for her and that she could rely on him. Sure, she'd claimed that she didn't need his protection but he vowed that he'd do just that for as long as they were partners.

All of a sudden, it was important that he find a way to let her know that she could trust him but in order to do that, he had to get her to open up to him, and for her to be able to do that, he had to show her how to talk to people outside of the squint squad and deal with situations outside of the Jeffersonian.

"You're right," he said again, more to himself than anything, but his next words were loud enough for Angela to overhear. "I'll take her to Wong Foo's for lunch and apologize."

His plan was met with a smirk but before he could say anything else, she said: "You will not regret trying, Booth. Brennan has a remarkably steep learning curve."

"So, I've heard," he muttered as he turned on his heel and made his way to the door.

"Booth?"

He turned to face Angela. "Yeah?"

"Don't forget to let her know when she gets something right, too."

He threw a small, grateful smile in her direction. "Thanks, Angela."