A/N: Here is the chapter you have all been waiting for! It's a long one as I couldn't find a suitable place to split it. Just a warning that there are some mature themes towards the end of this chapter although I think I have managed to keep it within the 'T' rating. I hope you all enjoy this chapter, there will probably only be one more chapter after this as there are a few loose ends left to tie up. I hope to have it written and posted this week before Christmas. Thank you once again for all your likes and reviews!

Disclaimer: I don't own Bones

Angela Montenegro was incredibly worried about her best friend. Brennan had come to the lab this morning to complete some paperwork. When she had walked in, Angela could clearly see that she had been crying and had tried to cover it with make-up. Anyone else wouldn't have noticed, but Angela knew. She had wanted to talk to her but got caught up with her own paperwork and by the time she had gotten around to going to find Brennan in her office, she was nowhere to be seen.

Angela had assumed that she had gone home again and she was a little hurt that Brennan would leave without saying goodbye, especially after not seeing her for a couple of weeks. But as Angela was leaving the lab to go grab some lunch, she spotted Brennan in the bone room examining an x-ray. Cases had dried up somewhat since Booth's injury and she knew that there were no remains in the bone room right now, so she wasn't sure what Brennan could be looking at.

"Hey, what're you doing in here Sweetie?" Angela asked as she approached her friend.

Brennan turned around and looked a little guiltily at Angela. She had been deliberately avoiding her. Angela knew her too well and Brennan didn't have the emotional energy right now to discuss what was happening with her and Booth.

"I'm just examining an x-ray of my arm. I wanted to make sure the fracture I sustained had healed correctly."

Angela chuckled "Only you would do that yourself instead of going back to see a doctor!"

"I know bones better than any hospital doctor, Angela." Brennan said, her voice full of disdain.

Angela laughed again and shook her head. "I know Sweetie. I was just going to grab a bite to eat if you feel like coming? There's a new deli down the street and their roasted vegetable wrap is to die for."

"I don't think so Ange." Brennan said as she switched off the monitor she'd been examining her x-ray on.

"Are you sure Sweetie? I feel like I haven't seen you in like, forever. I'd love to have a catch up."

Brennan shook her head "I'm sorry Angela, I really should be getting home to see if Booth is ok."

Angela took a moment to examine her friend. She had been different since Booth's injury. It reminded Angela of how Brennan used to be when she had first met her. It had taken Angela a long time to crack Brennan's tough exterior and even then, she had never managed to get her to open up like her charming, handsome, FBI agent partner did. What she saw in Brennan's face now though, wasn't just that hard exterior that she always used to have. Angela had detected a sadness in Brennan since Booth's accident, but now that sadness seemed to have intensified. There was a despondency to her that scared Angela.

"How is Booth?" Angela asked. Concerned that Brennan's feelings had been caused by Booth's condition getting worse rather than better.

"He's fine. He left the house yesterday without telling me and when I found him in the diner, he was flirting with one of his colleagues."

Angela was taken aback by what Brennan had just told her. It didn't sound like Booth, but then again, she knew he had been different since he woke up from his coma "I'm sure it wasn't what it looked like Sweetie."

Brennan was heartbroken about what had happened yesterday and when Angela asked how Booth was, she felt the urge to unburden herself. She knew though that Angela would not allow her to leave it at that and Brennan now regretted saying anything. "I don't want to talk about it, Angela. I really should get back." She turned to leave the room, but Angela grabbed her arm as she walked past her.

"What's going on, Brennan? I can tell something is up with you and I'm really worried. We all are."

Brennan considered telling Angela for a moment. The knowledge of what she was going to do was weighing heavily on her and she wanted relief from it, for just a moment. She knew though that Angela would talk her out of it, and it wouldn't be the right thing to do. She had to do it for Booth's happiness, even if it meant sacrificing her own. At that moment, her phone beeped in her hand. She looked down at it to see it was a message from Booth, asking her to meet him at the diner. She looked up again at her best friend, "I really have to go, Angela. Booth wants me to meet him."

Angela reluctantly dropped her hand from Brennan's arm. She knew she wasn't going to tell her anything else. She watched as Brennan left the room and felt a sinking feeling in her stomach. Something wasn't right. She headed back to her office instead of out for lunch. The conversation and the worry it had caused her had stolen her appetite and she could only hope that the nagging feeling she had that Brennan was going to do something stupid was wrong.

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Brennan made her way towards the diner feeling like her shoes were made of lead. She walked slowly, unconsciously putting off for a few extra minutes what she knew she had to do. As she walked through the door, she could see Booth sat at their usual table. Seeing him there made her doubt what she was about to say to him. She swallowed and took a deep breath before going to sit down opposite him.

"Hi." She said as she sat down, trying to decipher what the expression on his face meant. Brennan had never been particularly good at reading people, but Booth had been different. She had thought that she had gotten quite good at reading him, but right now, she had absolutely no idea what he was thinking. He didn't say anything which confused her even more. He looked kind of nervous to her which didn't make any sense.

"Is everything all right, Seeley?"

Booth smiled awkwardly and cringed at her use of his first name; for some reason, he didn't like it. He was feeling nervous. He felt like he was 16 again and about to ask the head cheerleader on a date. He reasoned that he was nervous because of what Sweets had said. Maybe he was afraid she would hurt him. He wasn't sure he would be able to tolerate the pain if she rejects him when he tells her he loves her.

He didn't just want to blurt out 'I love you', out of fear of freaking her out. Instead, he said "We need to talk, Temperance." They weren't the words he had planned to say when he saw her, but they were the words that had unexpectedly fallen from his lips. But unbeknown to him, they were the worst possible words he could have said to her.

Brennan immediately interpreted them to mean that he was having the same thoughts about their marriage that she was. That he didn't love her and wanted to be free to pursue a relationship with someone else. Reassured that her decision was likely what he wanted, she took a deep breath and ripped off the band aid.

"Yes, we do Seeley. I think we should separate."

Booth was momentarily dumbstruck. Had she just said what he thought she just said? "What?!" He managed to splutter. Despite worrying about her rejecting him, he hadn't truly believed that she would.

Brennan attempted to clarify and justify her decision to him. "I know you don't love me anymore Seeley, so I think it's for the best that we separate. That way, you are free to satisfy your biological urges in any way you see fit." Her voice wavered at the end as she fought back tears. There was a part of her that was screaming at her, questioning what the hell she was doing. But the rational part was overriding it, secure in the knowledge that it was the logical thing to do.

"Tempe, no. I don't want that! What're you talking about?" Booth said, shaking his head, appalled at what she was suggesting. How could she think he would want this? And 'biological urges?'-what the hell?

His use of the shortened form of her name only served as a painful reminder that he still hadn't remembered her. She had despised his nickname for her when he had first starting calling her 'Bones', but she now realised how special it was that only he called her that and how much now she would love to hear him call her by that name again. But she had to do this, his happiness was contingent on her being strong enough to leave. She bit her lip, trying to stop herself from crying. She got up from the table, the urge to flee too overwhelming this time.

"I'm sorry. I have to go."

She turned and bolted out of the door. She had expected to feel better, like a weight had been lifted. But she didn't, she felt worse. She now felt like a crushing weight was resting upon her chest and she couldn't breathe.

The weather had turned in the short time she had been in the diner and the previously blue sky was now dark with clouds that were pouring rain so heavy, it was like being stood under a shower. Brennan walked quickly back towards her car, pulling up her collar and bowing her head against the deluge of water.

Booth had been so startled by her unexpected words and sudden departure that he had just stayed sitting at the table, unsure of what to do next. He suddenly had another one of his déjà vu feelings. She had rejected him and then run from him before. His gut was telling him he couldn't let her do it again, not this time.

He jumped up from his seat and ran for the door. He looked both ways down the street and, through the rain, he could just see her striding away from him at the edge of the sidewalk. He took off running as fast as he could, dodging people as he ran. "Temperance! Temperance wait!"

She heard him calling her name and it made her footsteps falter. Automatically, she stopped and turned, trying to see him. But when she stopped, a large man that had been walking right behind her with an umbrella angled low as a shield against the downpour crashed right into her causing her to lose her balance and fall into the road straight into the path of an oncoming car.

"Bones!" Booth shouted when to his horror, he saw her fall into the road. He had managed to close the distance between them rapidly and with what he estimated was only a millisecond to spare, he grabbed her hand and yanked her back onto the sidewalk. She fell into his arms as the car sped past missing her by inches.

As Booth held her in his arms in the pouring rain, without warning he recalled a memory of saving her once before in similar circumstances. He remembered her being crouched down on the ground in the dark and pouring rain as he pulled her out of the way of a car that hadn't seen her until it was almost too late. He gasped as he was then suddenly assaulted by a barrage of memories of Bones.

"Booth!" Brennan exclaimed as Booth staggered backwards and she suddenly realised she was almost holding him up. She awkwardly shifted backwards a few steps with him so he could lean up against the wall of the nearby building. "Booth! What's wrong?" She was insanely worried. His face had gone blank and he seemed to be gasping for breath.

Booth felt like a thousand memories were running through his head. Too many to count or see clearly. Some stood out more than others, but they were all of her, his Bones. He could remember saving her so many times, saving her from Kenton the crooked FBI agent he had entrusted with her safety, digging in the dirt and pulling her from the hole in the ground after she'd been abducted by the Gravedigger, taking a bullet for her when crazy Pam Nunan tried to kill her. He could also remember being saved by her. Rescuing him from the ship that was about to explode when the Gravedigger had taken him, coming to save him with her father when he was being tortured by gang boss Gallagher, saving his life by making him seek help when he was hallucinating a cartoon baby when he had his brain tumour. There were so many other moments that stood out to him too. Delivering baby Christine himself in a barn, Bones asking him to marry her then the pain of having to renege on his response because of Pelant's threat. How he then asked her to marry him after killing Pelant, and their amazing wedding that nearly didn't happen after the church burnt down. So many memories. Booth was happy but he also felt intense regret. He realised now that she was more important than his memories. How could he not have seen what she had meant to him.

Booth took a breath to regain his composure and looked up to see Bones' worried eyes on his. He stood up straight and wrapped one arm around her waist while cupping her face with his other hand. Brennan could barely breathe as he held her in a way he hadn't done since before his injury. He stared into her eyes and she could see recognition and love shining in his.

"Bones" he whispered in wonderment before crushing his lips to hers. They kissed passionately, tasting each other as if for the first time. Booth broke the kiss and moved his hand from her waist to cup her face with both of his hands.

"Please don't leave me, Bones. I love you. I always have and I always will."

Brennan smiled as tears of joy and relief rolled down her face, mixing with the rain that was still pouring down on them both.

"I love you, Booth. I won't leave you if you don't want me to. I only suggested separating because I thought it would be what you wanted. I didn't think you would want to stay with me if you didn't love me anymore."

Booth felt tears stinging his eyes. He had hurt her far more than he had known. He didn't deserve her; she had sacrificed so much for him and was even willing to sacrifice her own happiness for his. "Bones, I'm so sorry that I forgot what you mean to me. I love you so much."

Brennan flung herself at her husband, wrapping her arms tightly around his waist. They stood there for a few minutes holding each other before Brennan could feel herself begin to shiver. "We need to go home, Booth. We're both soaked."

Booth pressed another brief kiss to her lips before saying "I'll go anywhere Bones, as long as it's with you."

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They quickly walked to Brennan's car and as she drove them home, she kept glancing at Booth who hadn't taken his eyes off her. It was as if he were worried that if he stopped watching her, she would disappear.

When they arrived home, they both quickly headed upstairs to their bathroom to strip off their wet clothes. Brennan was just about to unbutton her blouse when Booth stopped her, putting his hand over hers. "When is Max bringing Christine home?"

Brennan looked at him quizzically. "I was going to go and pick her up before dinner, why?"

Booth glanced at his watch then looked back at Bones. "Because I wanted to know if we had time to do this." He said before unbuttoning her blouse himself then kissing each piece of skin he revealed as he peeled the soaked blouse off her. He wanted and needed to show her just how much he loves her.

Brennan felt her breathing increase as she realised what his intention was. It had been so long since they'd made love and she had missed it greatly, but she was having difficulty absorbing how things had changed so quickly. Just an hour ago, she was preparing herself to leave him, and now, he was here, kissing her and taking off her clothes. However, the sensation of having his hands on her again scattered all rational thought and she gave herself over to her instincts and desire instead.

Brennan pushed his t shirt up, encouraging him to remove it before she released his belt buckle and the buttons on his jeans. She then slid her hands inside the waistband to push both his jeans and boxers down. Booth stepped out of his clothes then walked them both backwards to lay on the bed, kissing her anywhere he could reach.

Hovering over her, he began to kiss down her body. But Brennan grabbed his shoulders, urging him back up so his face was level with hers. She kissed him and wrapped her legs around his thighs drawing him towards her, urging him to make that most intimate connection. She was almost desperate to make this connection with him again. It was more than satisfying a biological urge, it was, as Booth had once told her, breaking the laws of physics, two people becoming one. She clung onto him, holding him close to her, almost not daring to believe it was real as he brought her to her release before finding his own.

They lay in bed afterwards, tangled in the sheets and each other's arms, sated and sweaty from their exertions. Booth lay there thinking about how thankful he was that he had managed to save Bones from getting hit by that car and that she hadn't left him. He didn't even want to think about what he would have done if he had lost her. He had been so close to losing her today, in more ways than one. As he was thinking, he felt something wet on his chest. As Brennan's face was resting on his chest, he could only assume it was a tear. He put his finger under her chin and tipped her face up to look at him.

"Hey, Bones. Why are you crying? Did I hurt you?" He didn't think he'd been rough with her, but he had been so lost in their love making, he couldn't be entirely sure.

Brennan shook her head "No Seeley, you didn't hurt me; it was wonderful."

"Then why are you crying?" The memory of her sobbing in this same bed yesterday was making her tears now all the more alarming to Booth.

"I… I nearly lost you." Brennan admitted, ashamed. She had been so close to leaving and then being hit by a car, but he had saved her once again.

Booth smiled to himself as he realised they had both been laid here contemplating the same thing. They were still as in tune with each other as they had always been. He kissed her softly then said "But you didn't Bones. I'm here now. We're here, together."

"Yes, we are Seeley."

Booth felt himself cringe again at her use of his first name and Brennan felt his body stiffen beneath her. "What is it?"

"Please stop calling me Seeley. I know I asked you to, but now I'm asking you to stop, unless you don't want to. It doesn't sound right; you've never called me that."

Brennan smiled and felt encouraged that her Booth seemed to be coming back. "Fine by me, Booth. On one condition, you stop calling me Tempe. You've always called me Bones and as much as I might have disliked it in the past, I find I missed hearing you call me by that name."

"Ok, Bones." Booth said with a grin before kissing her again.

Brennan didn't want to ruin the happy moment, but she knew they had to address everything that had happened today. "You know we need to talk about everything, don't you?"

Booth nodded "I know. But let's talk later and just enjoy this moment together now, huh?"

Brennan smiled and nodded her agreement before laying her head back on his chest, relishing the feeling of having him so close when she had thought she never would again.