Title:Prayer of Innocence

Pairing:Brennan/Booth

Rating:M

Disclaimer:I own nothing. Brennan and Booth are owned by FOX. Sadly Booth is not mine.

Authors Note:This is my first Bones Fanfic. Feedback welcome and wanted.

Chapter One

"Sweetie you need to get out here NOW!!!!"

Brennan was in her office when she heard the yelling coming from Angela. She put the x-rays she was looking at on her desk and made her way to Angela's office. Angela and Hodgins were standing in front of the TV in her office. They were both staring at it and did not even acknowledge the fact that she had joined them.

"Angela, I was in the middle of looking at the x-rays on the case that Booth and I working on I don't have time to be watching TV" Brennan hated TV. So many people wasted theirs lives sitting in front of that idiot box instead of living and experiencing life. She still hadn't replaced the one that had broken in her apartment although she had been meaning to. Not for her though. She had never missed it. Brennan moved to leave the office not understanding why Angela had wanted her to join them watching whatever it was they were focused on so intently.

"Special Agent Seeley Booth has been arrested today due to allegations of corruption"

Brennan froze. She looked to Angela for confirmation as if she couldn't believe what she had heard. Booth? Not Booth. He was one of the kindest and most dedicated FBI Agents she had ever dealt with and the only one who had been able to not only deal with her but understand her as well. Brennan forced her attention back to the TV.

"Details are still sketchy. Booth has recently made a name for himself working with the world renowned author and forensic anthropologist, Temperance Brennan. Join us tonight at six o'clock…" Angela shut of the TV.

"This can't be true. There is no way Booth would be crooked in any way" Angela was looking at Brennan looking for some type of reaction.

"I don't know what that means, but Booth would not be involved in anything illegal. He respects the work he does and is proud to be a member of the FBI." Brennan looked at Angela and Hodgins. Her mind was racing. There is no way that Booth would be involved. Although for the FBI to have actually arrested him there would have to be some evidence. Booth always wanted evidence before he would arrest anyone. That was what she was there for, to provide the evidence. Every part of her wanted to race down to the FBI office and demand that they tell her what was going on and to speak to Booth. The rational side of her knew that there was nothing that she could do and that she should just focus her attention back to the case at hand.

Hodgins looked at Angela. "Government conspiracy. They are framing him because he was getting too close to something he shouldn't. We all know that you can't trust them. I thought the FBI was a branch that had yet to be corrupted. I must have been wrong. I say we go down there and make them tell us what they are hiding." Angela placed her hand on Hodgin's arm. Brennan was staring at the TV which was now switched off.

"Sweetie?" Brennan didn't even notice that Angela had spoken to her and abruptly turned and left . She made her way back to her office. Sitting down she thought about what she had heard. She checked her phone and e-mail for any message from Booth. Nothing. Damm it. She looked back towards the X-ray on her desk. She tried to bring her mind back to the case she had been working on. However, some small part of her wasn't listening. Maybe it was this "gut" thing that Booth was always talking about to her. She had never really understood what he had meant by that. She always waited for the facts to provide the answers. No conjecture, no guess work. Evidence all the way. This was Booth though.

Does that mean she should be trusting the facts more than ever or should she be trusting her gut like Booth? This is what she needed him for. This is why Booth was her partner, her best friend. He understood her like no one else seemed to be able to. Brennan was so lost in her thoughts that she hadn't even noticed that Angela had walked into her office. "Brenn? Are you ok?"

"I don't know. This is a lot of information to process. I mean this is Booth." Brennan looked at Angela. "We don't know all the facts I can't believe anything without all the evidence. I am going down there."

"Do you think they will let you talk to him?"

" I don't know but Booth would do it for me." As Brennan spoke she realised it was true. Booth would never give up on her. He had not only defended her but saved her life on a number of occasions. Now she would do the same for him.

Chapter 2

Brennan picked up her bag and made her way to leave the Jeffersonian. As she made her way towards the exit, Brennan was pulled to one side by the guard.

"I am sorry Dr Brennan but we can't let you leave"

"What? I need to get to the FBI offices. I am working on a case I don't need to clear my schedule with you or anyone."

The guard simply nodded towards the doors. There were dozens of reporters being held off by security. It seemed as though the fact that Booth was her partner was enough for them to think that she was either involved or knew something about the situation they didn't. There was no way she was going out there. Brennan hated publicity. Since this story had broken her publicist had been on the phone. Brennan was disgusted at the words of "any publicity is good publicity" and that she should show her face as often as possibly and to mention her upcoming book a few times. Brennan had been sickened by the thought and had simply hung up and then switched her phone off. Booth was her priority. There was no way she was going to allow simple issues like her book to come in the way.

"Angela, ANGELA." Brennan yelled as she ran towards her office. "Brenn?" Angela caught up with as Brennan reached the doors of her office.

"There are reporters everywhere. I need to get to the FBI and there is no way I want them following me for the rest of the day. I am not a story and neither is Booth." Brennan looked towards Angela. "I need your help Ang. Can you help me get out of here without being seen?"

"I can't but I know someone who can. Give me ten mins."

Ten minutes later Brennan found herself seated in the back of a black stretch limousine. Angela had spoken to Hodgins and he had arranged for his driver to come and pick Brennan up from the delivery entrance of the Jeffersonian. The tinted windows allowed Brennan to be driven straight past the reporters without them being any wiser.

Brennan turned her mind back to the case that her and Booth had just started on. She had been working on her manuscript when her attention had been drawn to her doorway. Her best friend was leaning against the door frame holding a file in his hand. He looked fantastic as ever in his charcoal suits and outlandish ties. She stopped at his buckle. She always made herself stop at his belt buckle. Any further was not allowed, well not while he was looking at her.

"Let's go Bones."

That was all it took, those three words and her manuscript was forgotten as she grabbed her equipment and followed him out to his car. A skull had been found when the foundations of a building were being repaired. Further investigation had led to the discovery of the rest of the body. Booth had mentioned something about it being similar to a case he had studied back at the Academy. It was similar to some Mob hits that had occurred in the area. As they made their way back to the Jeffersonian Booth had told Brennan the story of how some crime syndicates would use new construction sites to dispose of the people they killed as it was rare for the foundations of a building to be pulled apart within a 20 year period of time and therefore their secrets would remained buried long enough for people to forget. Booth had dropped Brennan back at her offices for her to start looking into the cause of death while he was headed back to his office to find out more information in regards to the crime scene. "Go and have fun with them bones, Bones." She had rolled her eyes at those words. "Don't call me that. I will call you with an update before I leave". Those had been the last words she had spoken to him.

"Dr. Brennan. Dr. Brennan. What should I do?" Brennan focused her attention back to the driver who was indicating to the mass of reporters crowding around the front of the FBI building. She would think with all the things that happened in the world there would be more important issues for them to focus on then an agent being falsely accused of something he didn't do. The sensation behind FBI corruption and an author seemed to be worthy of more air time than the poverty suffered by millions all over the world.

"Go around to the right. There is a staff entrance on the side which should be a little less crowded." Brennan motioned to the driver finally answering his question. Brennan sighed in relief as she noted that the staff entrance was clear of reporters. The driver pulled over. He looked towards Brennan. "Master Hodgins has instructed that I wait here for you until you need to be taken back to the Jeffersonian. No matter what" Brennan nodded in thanks and made her way out of the limo and walked towards the staff entrance.

Brennan nodded towards the agent at the door. She pulled out her new visitor badge. Booth had finally got her one. It still said visitor but it had her name and her credentials and it was hers to keep. She had been complaining to Booth for the past year about having to sign in every time she went to the office. It had turned up on her desk last week. She hadn't even thanked him for it.

"I am sorry Dr. Brennan you can't enter today." Brennan shrugged the guards hand off her shoulder. She looked at him. "What?"

"I am under orders not to let you onto the FBI premises today"

"Whose orders?" Brennan could not believe this. If they thought she was going to just walk away they could think again.

"Cullen issued the order."

"Well you will just have to get Cullen down here to tell me that himself because I am not leaving."

"I am sorry. I can't do that."

Brennan looked around. Ok she had tried the rational approach and didn't seem to be getting anywhere. Ok let's be like Booth. Let's think like Booth. What would he do? Brennan looked around. A flash of light sparked in the corner of her eye. That's it.

"Look you either tell Cullen to get his ass down here or I will walk right up to those reporters and tell them all about my involvement with the FBI." The agent looked at her and picked up the phone next to him. She slowly started to back away from the agent and towards the reporters. She really did not want to have to do this. She hated the public but this was not about her anymore. This was about Booth.

"He is on his way down. If you wouldn't mind taking a seat Dr. Brennan." The agent opened the door to his office. Brennan sat down and waited. Why wouldn't they allow her in? She had never had this problem before. They must think that she was involved somehow. The fact that they even suspected Booth let alone arrested him indicated to her that they were the types to jump to conclusions before investigating the facts. Well she wasn't. There was no way she was going to accept them on their word. They might be the FBI but she was Temperance Brennan, Booth's partner and if they thought she would let this rest, they were wrong.

Chapter 3

"Dr. Brennan."

Brennan stood and looked at Booth's boss. "Deputy Director."

"I know why you are here and I am sorry I can not give you any information in regards to Booth's arrest. I am still trying to find out what the hell happened myself. I know as much as is being reported on the news."

Brennan looked at him. "Don't try and pull that one on me. He is my partner and there is no way that anything that is being reported in true. I want some answers. I want to speak to Booth."

"You can't talk to him. He was taken away by the Internal Affairs department last night. I have no information as to where he is being held or when he will be released. Trust me Dr. Brennan, I don't like this anymore than you do. One of my best agents has been accused of working for the bad guys and I have to deal with the media hype and irate scientists."

Brennan looked at Cullen and slumped back into the chair. So much had happened in the past few hours it felt like days. "Well what do I do?"

"Dr. Brennan. I need you to continue working on the case you were assigned with Booth. I have arranged for another agent to come and help you with the police work. You have worked with him before so there shouldn't be any problems." Cullen turned and walked out of the office. Before he made it to the safety of the security doors he turned back and looked at Brennan. "If I hear anything I will let you know." Brennan nodded at him and he continued back into the FBI offices.

Brennan slowly walked her way back to the limousine which was still waiting for her. She couldn't believe that there was nothing she could do. She knew that Booth could not be guilty but if his direct superior had no idea what was happening how would she ever be able to find him and help him. It wasn't until she sat down in the car that she realised what Cullen had said to her. An agent she had worked with before. Well there was only two other FBI agents she had worked with. Booth had shot one of them and the other had left months ago. Sully? Would Cullen have been able to convince him to return?

Although Brennan had been sorry to see Sully go she realised not long after that she did not really notice him missing from her life. There was no empty void. When her parents went missing there was a big hole in her and her life. When Russ disappeared with her father she felt like she had lost another part of herself that she had just got back. When Sully left, he just left. Ok, so she missed the sex. I mean it had been good but that was it. She didn't find herself wondering what he was doing, where he was. If she was really honest with herself, she had spent more time worrying about Booth in the past few hours than she had thought about Sully in past few months. What did that mean?

Brennan's phone rang drawing her away from her thoughts about her two FBI men. She looked at the ID. Rebecca Booth had insisted that she have her details and vice versa in case anything happened to him or if there was something wrong with Parker and Rebecca couldn't reach him. Brennan answered her phone. "Hi Rebecca."

"Yes I know I don't believe it either. I have just left the FBI office and they don't know where he has been taken."

"No I don't think you should tell Parker anything just yet. Wait till we have more information."

"Of course I will keep you updated. I will call you later tonight. I can't imagine I would have heard anything but I will call just the same. They have told me I need to continue on the case I was working on."

"Will I talk to Parker? Umm okay." What was she meant to say to Parker? She really was not good with kids.

"Hi Parker."

"Yes it's Dr. Bones." She was going to kill Booth when she found him. Now his kid was calling her Bones.

"Well Parker, the reason you can't talk to your Dad is that he is really busy at work but I will tell him that you say hello. I have a message for you though. You Dad says he loves you and misses you and can't wait to see you. Ok? Yes I will come and see you soon." What was she getting herself into?

"Ok Parker. Let me talk to your Mum again. Bye Parker."

"Rebecca I have to go. I just told Parker that his Dad was busy with work. I will call you tonight. Ok Bye."

Brennan looked at her phone. Still no messages. She looked out the window and realised that they were already back at the Jeffersonian. She had been so caught up with her thoughts and then the phone call to realise. The driver had brought her to the front of the building, the reporters had all dispersed. They were either tired of waiting around or something more exciting must have occurred. Brennan thanked the driver and before she got her hand on the door it was opened for her. As Brennan stepped out of the limo she noticed all of her associates were standing there expectantly awaiting news of Booth. She looked at them and shook her head. Brennan then looked at the person still holding open the door for her.

"Tempe"

"Sully"

Chapter 4

"Sweetie"

Brennan looked up from her desk Angela was standing in the doorway holding Chinese takeaway cartons.

"You need to eat. It is after nine and I know you didn't stop for lunch so you are going to eat"

Brennan sighed and nodded knowing that it was futile to argue with her friend when she heard that tone. Now that she thought about it she had to admit that she was starving. Skipping lunch hadn't been planned but with everything that had happened today it was the last thing on her mind. The sooner that she resolved this case the sooner she could turn her attention back to Booth. Cullen wanted her to concentrate on the case, and that's what she would do. Once it was finished though, it was going to be a different story. She was going to do everything possible to find out what had happened to Booth.

"So?"

"What Ange?"

"What happened with Sully? Are you guys back together now that he is back on the scene?"

"I don't know what you mean Angela." Brennan knew that this conversation was going to happen. Angela always looked out for her and helped her with her life. Although she was grateful, Brennan wasn't ready yet to share with Angela the feelings that had been racing through her today. So much had happened in such a short space of time. She hadn't allowed herself enough time to actually process all the facts and reach a conclusion. It seems as though today everyone just wanted answers from her.

Brennan walked briskly towards her office. No more talking. She knew that Sully was following her. She went to her desk and picked up the case file. Booth……Booth had left it there for her to go through.

"Tempe"

Brennan handed him the file.

"I haven't had a chance to closely analyse the bones yet. I have had a few other things to deal with today. I am going to finish up my analysis and we should have enough to have a face for you by tomorrow."

Brennan looked at Sully and then walked out of her office. As she made her way up to the lab she could see Sully leaving the building from the corner of her eye. Brennan released her breathe and relaxed. She hadn't realised how tense she was. Seeing Sully again had defiantly made a few things clearer in her head. There was no excitement, no fire. She was grateful that he had given her space. Everything had changed so much lately that Brennan wasn't sure what she wanted.

"Sweetie. What I meant was that are you going to be a couple again? The only reason you broke up was because he was leaving, if he is back then the reason you broke up is gone."

"I don't know Ange. So much has happened and I just don't know. I can't really think about this at the moment. I am completely swamped with my new manuscript and the case with the FBI still needs to be completed." Brennan looked away from Angela and placed her Chinese on the table. It hurt just to think about him. She needed to stay busy and focus on the things she could control. Her current feelings for Booth seemed to be something she couldn't control.

"Bren. It will be ok. We will solve this case and then we will figure what happened with Booth. He would not let us down and we won't let him down."

"I know. I just need to deal with one issue at a time. I just can't deal with Sully at the moment. While we are working together it will be strictly professional. He may not even be staying. This could be a one time deal." Brennan knew though that even if Sully did stay, things couldn't go back to the way they were. Him leaving her had forced Brennan to re-evaluate her life and the people in it. At the time she had felt that everyone who she let into her life would leave her, it had been happening since she was fifteen. Booth however had been one of the only constants in her life that she has been able to trust completely and who didn't make her feel as if she didn't fit in. He helped her become a better person and helped her understand people. He made her realise that he and her squints were her family. It may be unconventional, but a family they were just the same. She was not going to lose another member of her family.

"Well sweetie, with the way he was looking at you earlier I don't think he is going to like that."

Brennan looked at Angela but didn't bother responding. They sat there in silence and finished their food.

"Come on Bren. There is nothing more you can do here tonight. Go home and sleep."

"Ok." She just didn't have it in her to argue anymore today.