A/N: Thank you guys for the reviews and alerts. I know this is a tough story to read, but please have faith in me, I know where I'm going with this.

Song "Already Gone" by Kelly Clarkson

Remember all the things we wanted
Now all our memories, they're haunted
We were always meant to say goodbye
Even with our fists held high
It never would have work out right, yeah
We were never meant for do or die
I didn't want us to burn out
I didn't come here to hurt you now I can't stop

I want you to know
That it doesn't matter
Where we take this road
But someone's gotta go
And I want you to know
You couldn't have loved me better
But I want you to move on
So I'm already gone

Chapter 3

Booth stood still, he was petrified. He couldn't utter a word. She was putting him in solitary confinement. Why did he feel like someone else was dying? He was about to lose another precious piece of his life. The truth was he had already lost Brennan that fateful day four months ago. He had to see that now; he couldn't fool himself into believing she would ever be the same. He couldn't possibly expect things to be okay again, no matter how much he wanted it.

Brennan walked over to Angela's desk, away from the Angelator.

"Bones, tell me what you're feeling, maybe I can… maybe we can…"

"We can't." She turned on him. "No more! I can't be here for you now. I have to have breathing room. I feel like you have me under a microscope, like you analyze everything I do and say every single time I turn around your eyes are dissecting me. I need to breathe Booth!"

"I don't mean to do that!" Booth started the familiar mindless pacing, his hands expressed his frustration.

"Well, you do!" Brennan's voice was accusing.

"I'm worried! You're my wife! You… don't even seem like you anymore! You don't want me to care about that?" Booth's edgy tone set her off.

"No! I don't want you to care!"

"Why? How can I not care? My God Bones! Why are you pushing me away? We've always turned to each other! We were happ…" Booth's throat chocked on the word.

"Well, we aren't now. I need you to back off!" She hissed.

Booth's eyes flicked in denial. "Why? I'm your husband. I'm trying everything I know to be patient and understanding. I keep hoping you'll see how much I love you. I need you!"

"Well, I don't need you!" Brennan threw it in his face. She wouldn't be moved by his compassion. She had made up her mind.

"Since when? We were doing just fine. You didn't indicate anything was wrong before… and now when we should be holding each other and clinging to each other, you say get out of my face?"

"Everything is so easy for you, Booth." She shot back.

"Fine, then tell me what I didn't see!" Booth challenged.

"I don't owe you an explanation. And I don't owe you my presence at the Jeffersonian either," Brennan snapped. She knew what he said was true - they were probably the most happy and communicative they had ever been prior to Liz's death. After all the stresses, fears and worry, things had finally seemed to be going right for them, but now it was all over.

"Fine, you aren't going to be a Forensic Anthropologist, whatever!" Booth threw his hands up in the air in defeat. "So, what are you planning to do with all your time?"

"I'm going to be a mother to my son!"

"Well, Bones, he's in school. So exactly how is quitting this job going to help you accomplish that? You could go down to half days and still be there for our son!"

"This is what I want Booth!" Brennan wasn't about to be railroaded. There wouldn't be any compromises.

"Okay, fine! But Bones, that doesn't take away the fact that I'm very worried sick about you!"

"I don't need your concern, I need… I need to breathe, Booth!" Brennan said it with such conviction and yearning that Booth's eyes closed in surrender.

"Okay, whatever you want, Babe." He finally gave in. "You can stay home. But Bones, if we're having problems, we can go to a marriage counselor or a group for grieving parents… the books, they say…" He had read them all in desperation, searching for a way to touch her, to get her to talk to him. He ran out of options, there were no more things to suggest, because no matter what he said, it fell on deaf ears.

"I don't think you're getting this." Her voice was cold and condescending. She faced him, her legs were barely holding her up as the enormity of what she was about to do settled in the pit of her stomach.

"Okay?" Booth backed up a little bit; he needed the distance for what was coming. His eyes pleaded with her to come back to him.

"I want out of our partnership too."

He couldn't hear this, he wouldn't face it. He fought the temptation to cover his ears. "You can't mean that."

She looked up at him and felt beaten. She was war-torn from too many battles for survival. She took one last irrevocable step towards him. It was best this way; she needed to be free of it once and for all.

"I meant it." Her eyes left him no doubt. "I want to take some time out from the marriage too." Brennan said it fast, as though she could hardly believe it herself.

Booth's face registered the heartache she had just inflicted, but she was hardened to it. She would not let him get too close again. This was the end of the road for them. They had nowhere to go but their separate ways. She should had done this a long time ago, before… if she had, maybe there never would have been Liz… her guilt at even considering that possibility stopped any further thought of 'what if.'

Booth found his voice; his fighting spirit, though badly beaten, was not dead, "No, this is no way to deal with our loss, Bones, We have a son!" Booth reminded her needlessly, he was all she could focus on now.

"We had a daughter too!" She screamed. Brennan's tears fell. Why couldn't he just let her go and let her be? "I can't be with you right now. I can't give you anything anymore. I just don't have it in me, it's too hard, and it's too much. Please… Let me go Booth? Just let me go…" She pleaded with him to make it easy for her.

Booth couldn't think straight. What did he do wrong? Did she blame him for all of this? She had told him over and over not to blame himself. She would never know how much he did. In the first few days after Liz died, she had been more open, more willing to reach out to him as they lay sobbing in the dark. The bed held two broken hearted people who needed each other to keep breathing, but after the initial shock, things began to change. They helped each other those first days, leaned on each other, trying to make it through without falling apart completely, but he saw now that she had fallen. He hadn't been able to catch her; he had let her fall without noticing it. Now his hand was outstretched wanting to pull her back with all his strength, but she wouldn't lift a finger to help herself. All that was left was to watch her slip away from him.

Booth had opened his heart to this woman; he had given her the key to unlock every emotion, every feeling. Under her touch, he had been able to let down all the walls. She was inside of him, she knew everything about him, every detail. How could she just cut him out as though he were some kind of cancer? How could she let this happen to them, without even trying? His fury rose like a tidal wave inside; he tried to control it, because he knew it would only send her further away. How could she do this to them?

He took a long breath forcing it back. In a voice much calmer than he felt, he cajoled, "Bones, I love you. I need you. Do you think I care about anything other than you and our sons right now? Don't shut me out, please. I know what you are feeling. I know! The others, they have no idea, but do you think I don't feel this as much as you?"

"I don't care." Brennan's voice was devoid of emotion.

The wave was rolling back over him, blinding his vision, choking his breath. "You don't mean that." Booth stepped in front of her, as if to block her words.

"I want to move out… I need time to…" Brennan's words faltered as she saw the wrath forming on his face.

"What? And take Cooper?" Booth's mind could not wrap around that possibility. He wouldn't even consider it.

She remained quiet; she just nodded slightly.

"No! I'm not going to be separated from my son! It's enough that I only get to see Parker twice a month, now you are taking Cooper away from me too? How can do that now?" Booth wouldn't miss one minute with his little boy. He knew how precious time with him was.

"He needs me! Booth, you are never there, not enough anyway. You have been working too much, and I won't be working, and Cooper needs me!" She begged.

"But you can't do this!" Booth's voice was filled with anger.

"Living with you isn't working. I know we both lost her… but…"

"Bones... don't blame yourself!" Booth decided to put it out there. "Or do you blame me for her… it was on my watch." His voice was a hoarse croak.

"I don't have anyone to blame. I missed it. I missed saying goodbye. I missed it. You got to tell her everything." Her tears raced hotly down her cheeks. "You got the chance to say what was in your heart. You touched her, and held her. You said how much you loved her. I never had the chance to do that. She wanted me, you won't tell me, but I know! She asked for me, didn't she?"

Booth remained silent. He stepped back and leaned against the wall for strength; his legs felt wobbly, his heart felt skewered.

"I wasn't there! I was there when she was born." Brennan was pacing wildly as her brittle voice broke with memories. "I've been there every day since, and at that last moment, I wasn't there! I can't be there for you now. I can't make this less than it is, and say 'Hey, we still have each other'! Not again. Not this time. Surely you can understand that."

"No." Booth understood nothing anymore; everything was a mess.

"I should have been there. She was my baby girl! She was only five years old, and she needed me!" Brennan's voice was like steel.

"What? Is this about the fact that you went on the trip instead of me? You know that if I could have gone I would have, but Cullen made me stay and be there for the Martinez case. You were the only one who could have retrieved the bones and bring them back here. That's why you blame me, isn't it?" Booth asked trying to understand what was going on with his wife. Lately, she was a mystery of emotions.

"I told you I don't blame you, Booth!" Brennan answered, but Booth couldn't believe her, not when she wanted to leave him and take their son with her.

"Tell me then! Why in the hell are you doing this to me, Bones?" Booth's voice was racked with pain; he couldn't stand the thought of losing her too. Why was she punishing him this way?

"I'm not doing this to you, I have to…" She threw her hands out then brought them up to her neck as if she was chocking herself. "You smother me. You are always there." Brennan's hands indicated how inescapable it was. "I can't be your sidekick now. I can't be the person you lean on. I don't want to be. I need to find a way to go on with my life. I wish I was dead so I could be with her!" Brennan's voice cried out the truth.

The horror of finally hearing her thoughts scared the crap out of him. His fears were confirmed. "You still have us, you still have Cooper, Parker and me, and you don't mean that!"

"I do! I do! I want to be with her… so she isn't all alone! I don't know where she is." Brennan's hand went to her mouth trying to hold back the grief that was threatening to consume her. She had let it come barreling back. The numbness was gone, and she felt claustrophobic. The anguish was too much for her to bear. She tried to hold it back, keep it in the dark recesses of her mind and her heart, but it was coming out… No! She couldn't allow it to escape it now, especially not in front of Booth.

Booth made a move towards her, wanting to hold her.

Brennan flashed a warning look, and he stopped immediately. "You say she's in heaven! You keep telling Cooper that all the time, but I don't believe it Booth! I just don't!"

"If you don't believe she's in heaven, then where is she?" His words came out in the I'm-right-you-don't-know-what-you-are-talking-about way that she absolutely hated.

"Nowhere! She's nowhere!" The hopelessness resounded in her voice. The idea of her little doll gone forever, sent stabbing pain into her head. She couldn't tolerate this empty ache any longer. She had to stop it, bolt it out of her life. Booth was part of it. She couldn't deal with it anymore. He was connected to all the pain, so he had to go too. Shoving him away was the only answer. It was the only way the numb comforting illusion could stay.

"Bones…" Booth kept trying to reach her; he needed her to be with him. "I don't care about the job, if you never want to be a Forensic Anthropologist again, I don't give a damn about the Jeffersonian! But our marriage? How can you just leave? Leave me? You expect me to let you go without a fight? And what about Cooper? Don't ask me to live without him, not now! I'll do anything… anything! Don't do this to us… we can get through this." Booth's hands pleaded with her as his eyes denied this cruelty.

"I can't!" Brennan cried out. There was still a small part of her that wanted to bury her head in his chest, and cling to him forever. Another part that was motivating every move, every reaction, took over. That was the part that was cold and unfeeling, becoming filled with bitterness. And yes, blaming him for what was entirely not his fault. But she had to blame someone more tangible than God.

"You don't love me anymore?" Booth asked. Now, when he needed her so desperately, how could she turn away from him?

"I don't feel anything…" Brennan told him the truth.

"You… You don't?" He asked shocked. "I do… I love you… I feel like everything inside of me is dying all over again. We lost our little girl, and now I'm about to lose you too, Bones? Why? Why are you doing this to us? We're a family! For God's sake! Talk to me! Yell at me if you have to! Kick me, I don't care! Just don't walk away!" His voice broke. The look on her face told him it was useless to beg, but he couldn't' give up.

She looked at him, giving him one second of the old Brennan, "When my parents abandoned me, I thought my life was over. Then years later, I found out my mother was murdered, and that was the most painful thing I had ever faced. I didn't think anyone could ever go through anything worst than losing a parent, but I was wrong, there is nothing worse than losing a child, and you should know that too." She shouldn't need to explain that to him; he knew how painful it was to lose their little girl.

Tears formed in his eyes. He reached for her in one last ditch effort to save her, to save them, to save his family. She saw the agony on his face. In spite of the fact that she felt nothing but the need to escape him, she allowed him to pull her into his arms.

He let it all go at last. He had put up the strong 'I'm a man front', and he had allowed himself little emotion after that first day. To give into it would be his ultimate downfall. Once he allowed the tears to start, he knew they would never stop. His body shook with sobs as his head rested on hers. She hugged him out of habit, not out of mutual need, not even sympathy, or empathy. It was a mechanical gesture, not the love of a wife trying to be there for her husband. She couldn't remember the last time she felt that.

Booth's sobs subsided, as he felt the distance still separating them. He stepped back, not letting go. Brennan's arms dropped to her side. She stared up at him, expressionless.

"What's happening to us?" His voice was raw with emotion.

"I don't know." Brennan answered woodenly.

"I love you!" Booth said it, meaning every word. "I know you love me too. I know you do!"

"Do you? Well, then I guess everything is just perfect!"Brennan shrugged off his arms from her shoulders, stepping back and took an irrevocable step away from him. "I want a legal separation." She wouldn't look at his eyes. Those damn eyes of his. She hated them. They reminded of her little girl. Emotions wouldn't stay buried if she had to look into those eyes everyday. She wouldn't be able to escape them, and she was determined to never face them again.

He felt it again. The urge to shake her, to grab her and shake the living daylight out of her. His own anger escalated as the realization of what she wanted hit him. She was deserting him! She, who had stood by his side from day one, was now turning her back on him, and taking the one joy he had left - his son.

"So you want to end all of our partnerships. Why do you think not coming to work every day, not facing me every day is going to make this easier? It won't. Trust me, Bones, it won't. This is not the answer. I know you are hurting now, I know you want to punish yourself. I've seen you on this path, hell bent on destroying everything. What is it, babe? You think destroying me is the best way for you to pay?"

"This isn't about you, Booth. Not everything is about you! I'm doing this because I need to for me."

"Is this for our son too? You think he's better off without me too?"

"No, of course not, you can see him whenever you want." Brennan's voice softened.

"I want to see him every day! Every morning, every night when I get home from work, and all my weekends. I want my son to live with me." His voice cracked in misery, just picturing those days and nights without his son was too much to handle. He couldn't imagine being without him, not after his sweet little Liz. "I miss her, Bones. Please don't take him away from me too."

"I need time Booth."

"Okay, time. I can give you time… but not distance. The house is huge. I can move to the guest bedroom, if you want. I will leave you alone, I won't push, and I won't expect anything. Bones, please don't make me leave! If I've been too close, it's because I'm terrified for you, for us, for our son!"

"It wouldn't work… Booth, you push even when you don't know you are. This is how you are, and I can't deal with it anymore. I have to do what's best for me. You just never seem to understand that." Brennan was speaking from years of frustration over trying to get inside of Booth's head. She tried so hard to find out what made him tick that she had forgotten what made her happy. He took too much energy. She was exhausted. She just couldn't play the game anymore. It was over.

"I… I just wanted you to turn to me. I'll do anything, Bones… Anything!" Booth was pleading, he would fall to his knees and beg if he had to, and he wouldn't let her go that easily.

She knew she could give in again, but happy was over. Now they were going through the motions. She wouldn't put him first anymore. She had happily in the past, but maybe that was why she was so lost now. Making anyone the center of your universe was a mistake, the sure road to unending heartache. She needed the air to breathe and the space to heal, if that was even possible.

"No" She said with finality. "You have to go, or I will. I'll wait to file the separation papers, but it's…" She couldn't hurt him anymore. Some part of her protected him in spite of her resolve to be selfish. Nothing made any sense anymore.

"As for Cooper, you can see him anytime; you can take him with you for overnights. I have to do this, Booth. I'm not sure for how long, or if I will ever want to go back." Brennan knew she would never go back; she could never open herself to any more devastation. Enough was enough.

Booth bowed his head. Digesting this was like swallowing a vial of poison. He felt it snaking its way into his body, contaminating him inside and out.

She finally glanced up into his eyes, then looking down quickly. "I have to go. I can move out by the weekend."

Booth answered as if in a trance. His voice sounded as if it was coming from a tunnel, a very dark tunnel. "No. I will move out. Cooper needs familiar surroundings now. He's already lost his sister, and now I won't be there. He needs to have the security of his home."

"FINE." Brennan answered too fast and then she remembered her manners, always be polite. "Thanks." She felt strangely relieved, like a big weight had fallen off her. She had decided over a week ago, and now it was done.

Booth watched as she left Angela's office. He tried to think of something more to change her mind, and yet he was too numb and unable to open his mouth to utter a word. He felt the fight go out of him, and suddenly she was gone.

As the door shut behind her, Booth couldn't breathe. She took the air with her, and he was choked by the constriction of his chest. He sank into Angela's chair, burying his head in his hands. Now he had lost everything. He heard the door softly opening, and he had no illusion that it was Brennan coming back, changing her mind, saying that she wanted him back, that she needed him, that she couldn't do this alone, and that she couldn't take Cooper out of his life.

The soft hand massaged his shoulder, quietly whispering to him that all was not lost. "It's going to be okay Booth. She will come back." Angela soothed him, like the dear friend that she had always been to him, to both of them. But now, no one could help them. Brennan had isolated herself. She didn't want anyone's help, and no one could save her.

His tearful eyes sadly rejected her words.

"She asked me to move out. She asked me for a legal separation."

A/N: Thank you for reading. Please tell me what you think by so far? Good/bad? Sad? I would love to hear what you guys think. Another chapter should be up soon.