Author's Note: It's been years since I have read or written Fanfiction but recently started watching Bones again on Hulu & felt the need to write this. It starts out following the show, set directly after "The Doctor in the Photo" but goes it's own direction after that. Will start out as Booth/Hannah but will end up B&B all the way. Not sure yet if this will be a B&B friendship or B&B romance.

It's rated T for now, but may go up to M in later chapters. Depending exactly what direction I take this.

Warning: This may or may not end up as a happy story in the end, but it certainly will not start out that way. You have been warned. There will be mentions of possible sexual assault, which may be explored further in later chapters.

I do NOT own Bones!

"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.

Booth look at Bones, at the road in front of him, then almost nervously back at Bones. "I'm with someone, Bones... & Hannah, she's not a consolation prize. I love her." Booth said quietly.

That was it, that was all it took for Brennan to break. This case had been extremely hard on her. It took so much courage for her to finally tell Booth how she really felt. It was at that instant, the tears started to fall freely.

A wave of guilt rushed over Booth. All these years, Booth had been the one to protect her. He had spent years trying to break down her walls, to get her to let him in. 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.

"You know, the last thing I want to do is hurt you... but those are the facts." Booth stated. Unsure of what ever to say.

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.

Brennan was unable to stop the tears from falling.

"Do you... want me to have someone stay with you?" Booth asked, concerned for his best friend.

"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. She had missed her chance. Booth had loved her & she had hurt him when she pushed him away that night after recounting their first case to Sweets. Brennan hadn't understood just how much that kind of rejection could possibly hurt, until tonight.

Once they reached their destination, they quietly parted ways. Booth watching Brennan intently as he drove away.

Booth headed back to his apartment, to Hannah... but his mind 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. She was his partner, his best friend. She had been there for him so many times, through so many things. It killed him to leave her like that. Still, Booth was with Hannah now & just because Bones suddenly had a change of heart... that didn't mean he could just leave Hannah. Truth was, Booth did love Hannah... but he also loved Bones. He had always loved Bones. He felt so torn as he drove away.

However, at that moment Booth had no idea that may be the very last time he ever saw his partner & best friend...

Brennan went back to her apartment that night & then, returned to the lab... after she had composed herself some. It wasn't like Brennan to just break down like that & 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 & I lost it. That was my fault, not Booth's. Of course, Booth isn't going to leave Hannah for me. It's my fault... Booth loved me once. He wanted to give us a try & 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 got a cab & returned to her apartment. Exhausted, physically & mentally... she needed to get some rest in order to ready herself for the following day. She still wasn't sure how she was going to face Booth in the morning.

Brennan unlocked the door of her apartment just as she did every night. Nothing seemed out of the ordinary. She didn't get any feeling that anything was wrong. She opened the door & reached for the light but it didn't come on. She sighed & headed across the room to find another light switch.

"Looking for something?" an unfamilar 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."

Brennan stopped dead in her tracks, her heart beat suddenly pounding so hard it felt as though it were in her throat.

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

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

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

Brennan kneed the unknown intruder in the balls & 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 & head. 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. That's when it all went black...

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 the Lab?"

"I haven't seen her all morning, I called her cell but it went straight to voicemail." Cam explained.

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 & not taking phone calls."

Booth's heart sunk. He has placed several calls to Bones himself that morning but they had gone unanswered. It was not at all like Bones to not come to work, especially not like 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 am 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 & 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 & Booth couldn't get the images of her crying in his car the night before out of his head.

"Tell you what, give this to Hodges. I am going to go check on Bones." Booth said.

"Will do." said Cam.

Booth flew to Bones apartment. 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 & near begged her to give their relationship a chance. Bones refused & 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, images of Bones crying... no, sobbing, in his car 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 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 apartment was ransacked. Furniture was overturned, there was broken glass all over the place. Booth looked down & 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, as he quickly ran through the apartment, gun drawn, clearing ever room.

Bones was no where to be found. It was obvious there was a struggle. She had fought back. After clearing the apartment, Booth walked back towards the door & the puddle of blood he had found on the floor. It was then he noticed a trail of blood drops that went through he apartment. He followed them, until in the hallway, he found something that made his heart sink even more. It was the shirt that Bones had been wearing the night before, there was blood on it & it was clearly torn as though it had been ripped off. Booth continued to follow the blood trail to another room, Bone's bedroom... where he found he pants thrown on the floor on the side of the bed. An alarm clock lay on the floor, next to a broken lamp... & 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 was blood drops at the head of the bed & 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 & 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". Suddenly, so many emotions flooded over him... hurt, guilt, sadness, anger.

Booth called for backup & then 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.

What did ya'll think? Please read & review! Comments are welcome!