Author's Note: This is a revamp of a story that I started some years ago, but never got around to finishing. I have every intention of finishing this story! I'm also editing the original chapters, adding additional content, etc.

This is a dark story that takes place directly following Episode 6x09 The Doctor in the Photo, but goes it's own direction after that. Still reeling from the emotional events of that stormy night, Booth wakes to find that his partner is missing, gone without a trace... the apparent victim of an unknown stranger. While the team is desperate in the search to bring their friend home, Bones is trapped in a living hell.

This is a bit of a psychological thriller, if you will. Very dark, emotional, raw... deals with adult themes, abuse, sexual assault. Proceed at your own risk! You have been warned!

The thunder rolled, lightning shot across the night sky, the wind blew and rain poured down, hitting hard on the windshield of Booth's SUV. Inside Brennan's head, another storm, one just as violent as the storm they were caught in, brewed.

This case had taken a very real, very emotional toll on Brennan. Booth certainly had noticed this, but he hadn't quite understood why. Their drive, thus so far, had been silent... it was an almost awkward silent.

Booth had followed Brennan that night, fearing for her safety and worried about her current mental state. In doing so, he ended up saving her from being hit by a vehicle, just as she'd solved the case. Now that the case had been solved, Booth hoped that his partner would be okay once more. He wasn't used to seeing her like this, as she had been these past few days... it was totally out of character for her. Honesty, seeing his partner so emotional, so... fragile, scared Booth far more than he'd like to admit. It was almost as though something inside of her had snapped.

Booth was suddenly pulled from his thoughts, when Brennan finally broke the uncomfortable silence that consumed them.

"I got the signal Booth. I don't want to have any regrets..." Brennan said, nervously looking to Booth for an answer, for the understanding she hoped he had.

Brennan had never been good with psychology or dealing with her feelings. Booth always seemed to be able to help her with that, always lending advice... whether she wanted it or not. He had always been her rock, her hero... almost. This case had made Brennan realize, just what she was missing in her life. It had made her realize that, no matter what she'd tried to tell herself... she did indeed love Booth. Pushing him away as she had in the past, when he'd confessed his feelings for her... when he'd almost begged her to give their potential relationship a shot, had been a mistake. Tonight, that was so clear. She just needed him to know...

Booth looked at Bones, at the road in front of him, then... almost nervously, back at Bones again. For an instant, Brennan wasn't sure if Booth understood what she was referring to, but what came next, told her that he did understand exactly what she meant...

"I'm with someone, Bones... and Hannah, she's not a consolation prize. I love her." Booth said quietly, swallowing the lump that had instantly formed in his throat.

That was it, that was all it took for Brennan to break... all the built up emotions from the past few days finally boiled over. Though she tried hard to hold it back, she felt as though her whole world was crashing down around her, in that moment. This case had been extremely hard. It took so much courage for her to finally tell Booth how she really felt. It was at that instant, hearing Booth's words of rejection, that the tears started to fall freely.

A wave of guilt rushed over Booth, immediately. All these years, Booth had been the one constant in her life, the one to protect her. He had spent years trying to break down her walls, trying to get her to let him in, trying to show her that he was there for her and he wasn't going anywhere. And now, now he had to do the very last thing he ever wanted to do. He had to hurt her... just as everyone else in her life had done.

Booth swallowed hard, not knowing exactly what to do or how to proceed. Normally, when Bones was upset... he would pull her into his arms, into one of his famous "guy hugs", but now... with the weight of knowing full well that he was the one causing her pain, causing her tears... it was breaking him inside, he just felt so small, so lost.

"You know, the last thing I want to do is hurt you... but those are the facts." Booth stated, finally. He kept he gaze focused firmly on the road ahead of him. In that moment, he knew... if their eyes met, he would end up doing something that he'd regret. Well, maybe "regret" wasn't the right word... he'd do something that was "wrong" because he was with Hannah, after all.

Brennan let out a defeated sigh. "I understand... I missed my chance." She said, trying hard to hold back a sob that was threatening to escape her lips. "My whole world turned upside down... I can adjust."

"I did." Booth said.

"Yes, you did." Brennan replied, matter of factly.

Brennan was unable to stop the tears from falling, now. This, being so emotional, wasn't at all like her...

"Do you... want me to have someone stay with you?" Booth asked, his heart breaking for his best friend. He too, wanted to cry.

"No, I'm fine... alone." Brennan replied.

The remainder of the ride was quiet, awkward. The pain Brennan felt at that moment was almost too much to bear. She tried, desperately to stop the tears from falling. The fact that she was trapped in a vehicle with the one who had caused her all this pain, made the feeling even worse. Being so close to Booth, literally inches apart, yet... it felt as though they were worlds apart in that moment.

She had missed her chance. Booth had loved her and she had hurt him deeply when she pushed him away, that night on the steps of the Lincoln Memorial... after recounting their first case to Sweets. Brennan hadn't truly understood just how much that kind of rejection could possibly hurt, until tonight.

Once they reached their destination, they quietly parted ways. Brennan exited the vehicle quickly, without another word to Booth.

"Bones..." Booth said, softly, as his partner was about to close the door. "Are you sure you'll be alright? I can call Angela..."

"I'm fine, Booth." Brennan replied sharply, before quickly closing the door behind her... running towards her apartment.

Booth watched Brennan intently, as she headed towards her apartment, through the rain that was still pouring down with a vengeance. He let out a heavy sigh, roughly running his hand across his cheek, into his hair.

As the storm raged on, Booth got a strange feeling... it felt like his whole world was crashing down, just like the rain pounding onto his windshield. Booth had the strong urge to follow Bones to her apartment. Deep down, he knew that she shouldn't be alone, right now. However, the truth was... Booth didn't fully trust himself to be alone with her, right now either. He was with Hannah, after all... but despite what he had told Bones after her emotional confession, he still had very strong feelings for his partner. The truth was, those feelings... they had never went away. Not really. It was the heart break of being rejected by Brennan, that had pushed him into the arms of Hannah in the first place. It had started as his "distraction" fueled by lust and loneliness, however, somewhere along the way... that "lust" had turned into feelings. Booth did love Hannah, at least he thought he did. Still, deep down... he knew that Bones needed him now, more than ever.

That feeling made his stomach twist in knots. The only thing Booth wanted to do, right now, was go to Bones... to comfort her, to talk, to make sure that she was alright. Booth couldn't do that to Hannah though, he couldn't go to Brennan now... because emotions were running high, everything was so raw tonight, feelings were at the surface... it would be too easy for things to "happen", right now.

Finally, after sitting in front of Bones' apartment building for several minutes, deep in thought, Booth slowly drove away.

He headed back to his apartment, to Hannah... but his mind still could not stop replaying the words Bones had said to him. A tear slipped down his cheek. Booth had always promised to be there for her, to protect her. Booth had spend years trying to show Bones that he, above anyone else, would never hurt her. That he would always be there for her, no matter what. She was his partner, his best friend, and so much more. The truth was, he didn't even really know how to describe their relationship... as it was unlike any he'd ever shared with anyone else in his life. She had been there for him so many times, through so many things... just as he had for her. It killed him to leave her like that, absolutely killed him... crushed him in ways he never knew existed.

Still, Booth was with Hannah now and just because Bones suddenly had a change of heart... that didn't mean he could just leave Hannah. Truth was, Booth probably did love Hannah... but deep down, he knew... he loved Bones more. He had always loved Bones. He felt so torn, this was going to be a long night...

Brennan went back to her apartment that night, but only briefly. Then, returned to the lab... after she had composed herself some. That's how Brennan had always dealt with her emotions, by throwing herself into her work. It wasn't like Brennan to just break down like that and it wasn't like her to put down her walls either. She had built those walls for good reason. It seemed that every time she put them down, she ended up getting hurt.

"What was I thinking? Did I really think that Booth was going to welcome me with open arms? I had my chance and I lost it. That was my fault, not Booth's. Of course, Booth isn't going to leave Hannah for me. Booth is a good man, he would never do that. It's my fault... Booth loved me once. He wanted to give us a try and I pushed him away. He's moved on now... I'm not sure how I can move on from this? I'm not sure how I can face Booth tomorrow..."

Sometime around 4:00AM, Brennan left the lab. She caught a cab and returned to her apartment. Exhausted, physically and mentally, she needed to get some rest in order to ready herself for the following day... which was already beginning. She still wasn't sure how she was going to face Booth in just a few short hours. Her mind was whirling.

Brennan unlocked the door of her apartment, just as she did earlier that night and every night. Nothing seemed out of the ordinary. She didn't get any feeling that anything was amiss. She opened the door and reached for the light switch, but it didn't come on. She sighed... just another thing to go wrong tonight. She walked across the dark room, reaching for the other light switch, when something stopped her dead in her tracks.

"Looking for something?" an unfamiliar voice said, from the darkness. "You won't find it, Dr. Brennan, the power to your apartment has been... let's just say it's been... cut."

Immediately, Brennan's heart was racing... pounding so hard, it felt as though it were in her throat.

"Who's there? What do you want?" Brennan said, nervously. Trying to keep the fear she felt from escaping through her words.

Before she could move or take another step, an arm was roughly wrapped around her neck, pushing on her throat. She felt the sharpness of a knife blade pushing into her neck.

"I want you, Dr. Brennan" the voice said. "I want you."

Everything happened so fast, Brennan was absolutely terrified. The only thing she knew, right now, was that she had to fight. Acting quickly, Brennan kneed the unknown intruder in the testicles and tried to run, but it took only moments before she was tackled to the ground. He punched her once, twice, three times in the face and head. Her body hit the floor with a hard thud. She felt her blood running from her nose, she could taste it on her lips. Then, in an instant, his hands were wrapped tightly around her neck... draining the life from her body. She tried to fight him, but he was just too strong. That's when it all went black...

A few hours later, the Lab was busy and bustling. Angela was in her office, working on a sketch when Cam walked in.

"Good Morning, Angela!" Cam announced. "Have you seen Dr. Brennan?"

Angela shook her head. "No, why? Isn't she in her office?"

"No, I haven't seen her all morning, I called her cell but it went straight to voicemail." Cam explained, the concern was evident in her voice.

Angel looked puzzled. "That's strange, very strange." she replied.

Suddenly, Booth walked in.

"Hey, have either of you seen Bones? We have a case." Booth asked.

"No, actually we haven't." Cam replied. "She's not here and not taking phone calls."

Booth's heart sank. He had placed several calls to Bones himself that morning, but they had all gone unanswered. It was not at all like Bones to not come into work, it was especially unlike her to not even call or answer a call. Had he really hurt her that much the night before?

"Are you okay, Booth?" Cam asked, concerned.

"Uh yeah, yeah Cam... I'm fine." Booth replied. "Just a little worried about Bones."

"This case has been really hard for Bren." Angela said. "I know she hasn't been sleeping, so... maybe she's just getting some rest. I'm sure she just overslept and will be here, totally freaking out about it, any minute."

"That still doesn't sound like Dr. Brennan." Cam said.

"I know... but she really hasn't been acting herself since the last case started." Angela said. "I am very worried about her, but she won't let me in."

Booth handed the file he was carrying to Cam. Their last case had been very hard on Bones and Booth couldn't get the images of her crying in his SUV the night before, out of his head. He had to go over to her apartment and make sure that she was alright.

"Tell you what, give this to Hodges. I am going to go check on Bones." Booth said, before quickly rushing out of the Lab.

"Will do." Cam said, but he was gone before she even got the first word out.

Booth practically flew to Bones apartment, driving as fast as he could. His mind full of guilt, his heart full of hurt... though he wasn't sure quite why. Booth had confessed his feelings for Bones in the past. He had kissed her and near begged her to give their relationship a chance. Bones had refused and he had told her that night, that he would have to move on. Now he had, with Hannah. Bones, of all people should understand that.

Still, the images of Bones crying... no, sobbing, the night before... just broke his heart. How could I leave her like that? Booth mentally cursed to himself. I promised to be there for her. To protect her... not hurt her! He knew that even though Bones had assured him that she was fine the night before, he should not have left her alone. Not like that. Booth was almost afraid to go to Bones' apartment. What if she didn't want to see him? What if the reason she wasn't at work or taking calls, was because she couldn't stand to be around him at all? Many different theories were running through Booth's mind, but in the back of his head... he felt that something just wasn't right. He just had a really bad feeling about this.

When Booth arrived at Bones' apartment, he immediately knew something was very wrong. When he knocked on the door, it slid open. As he entered, he knew right away that something very bad had taken place there. Swallowing hard, Booth slowly entered the apartment, gun drawn. The apartment was totally ransacked. Furniture was overturned, there was broken glass all over the place. Booth looked down and that's when he saw them... Bones' keys... laying on the floor, beside a small puddle of blood. Booth's heart sank.

"Bones! Bones!" Booth called frantically, as he ran through the apartment, gun drawn, clearing every room. Booth called in, requesting a backup unit to the apartment.

Bones was no where to be found. It was obvious that there was a struggle. She had fought back. After clearing the apartment, Booth walked back towards the door and the puddle of blood he had found on the floor. It was then he noticed a trail of blood drops that went through the apartment. He followed them, until in the hallway, he found something that made his heart sink even more. He felt as though he was going to be sick. It was the shirt that Bones had been wearing the night before, there was blood on it and it was clearly torn as though it had been ripped off in a vicious attack. Booth continued to follow the blood trail to another room, Bone's bedroom... where he found her pants thrown on the floor, on the side of the bed. An alarm clock lay on the floor, next to a broken lamp... and a pair of underwear.

"God no..." Booth said, so quietly it was barely a whisper.

Booth carefully pulled back a pile of mangled blankets from the bed. There were blood drops at the head of the bed and a large blood stain towards the bottom. That's when he saw her phone, laying on the floor, on the other side of the bed. Booth pressed it on and seen that Contacts were open. The name of the person she was trying to dial, when the phone was somehow thrown to the floor... was "Booth". So many emotions flooded over him... hurt, guilt, sadness, anger.

Booth had already called for backup, now he called Cam. Barely able to keep the tears that had welled up in his eyes from falling.

"Cam, it's Booth...something bad happened to Bones..." Booth said, the last part turning to a whisper.

TBC...

What do y'all think?