Tick-tock, the ugly clock in Jeffersonian was inexorable, the time was unforgiving and even though Booth wouldn't let anyone give up, deep down he knew they were too late. It's been hours since the Gravedigger took Hodgins and Brennan, none of them took a break even for one minute, they tried everything they could, the press didn't work, the search was useless but Booth couldn't give up, he just couldn't.
He was thinking how he let his partner down, how he should have been there to protect her, he looked at Angela who had the same expression on her face as he was sure he had, they exchanged glances and didn't need words to express what was between them. Hodgins and Bones were theirs, in every sense, they belonged with them even though it was still work in progress. Involuntarily, Booth's mind was going back to their very first case, when he met Brennan in that lecture room. He remembered every second, when he saw for the very first time and the world stood still, he remembered her kiss and their ridiculous fight. For the last year Booth was pushing away those memories for the sake of their partnership and friendship and he knew that Bones was doing the same thing, it was their unspoken agreement, their romance didn't work out, but their friendship did. In spite of that, deep down, Booth still knew that Bones belonged with him and that one day they would catch each other. But now…No, he won't give up, Hodgins and Bones were geniuses, they would have found a way to extend their air supply and even if they don't…He couldn't think about it, not yet.
His phone rang and he jumped as if he was burnt, he got a message from Bones! She was alive! He rushed to Cam and they were trying to figure out what was it about, about ten minutes later Zack got it, he calculated where they were buried and they rushed there as fast as they could.
The place was a vast excavating sight, with no trace of tracks or anything really, still they began the search, Booth was praying with everything he had that they would make it on time, he, Zack and Angela joined the search team, while Cam was trying to navigate things. It took them five hours before one of the techs yelled that they found something. Not feeling the ground under his feet Booth ran towards the tech, they were digging as fast as they could. Shortly, they saw Bones' car, Booth and Angela were especially impatient they yelled their names hoping to hear the response, when the car was finally more or less clean, Booth opened the one of the doors. His heart was frozen with fear and hope, Bones and Hodgins were silent, holding hands at the backseat, their eyes closed and it looked like they were sleeping. They probably were unconscious since it took their team way too long to find them. As soon as he reached his partner's hand, he knew it was over. Everything went dark, all he could hear his own voice yelling Bones' name again and again, but there was no response, no snotty remark on why it took so long for him to find her, she was gone.
Their bodies were transferred to Jeffersonian, Angela had a breakdown right there, unable to hold it together anymore. Cam refused to perform the autopsy, Hodgins and Brennan looked almost alive and it was impossible for her to do this to them, so they waited for another coroner to arrive. If it wasn't for the first signs of rigor mortis, they would look as if they were in a deep sleep. Booth was trying to keep it together, but his eyes were wet, his hands were shaking and all he could see the serene face of Bones. He needed to find who did this, that's the only thing he could focus on. If necessary, he will dedicate the rest of his life to this search.
Zack was sifting through evidence, their bags and what was left of the car. He found the bloody knife, the wires and burnt phone, the empty bottle of what looked like perfume, the bunch of Bones' pens and her book. He opened it and found a small piece of bumper stick; it was bloody too. Zack immediately took it for examination. While the scientist stared through the microscope, Booth noticed some pages in the book were cramped. He opened Bones' book and found pieces of paper. One was signed by messy handwriting: Angela. The second one was neatly folded and Booth knew it was Bones' note, only she would fold the piece of paper so neatly even in those horrifying circumstances. He called Angela and gave her Hodgins' message, she was crying non-stop for the past hour. Brennan was her best friend and Hodgins…Hodgins was something she was trying to figure out. She took the note and went to her office, clearly needing some privacy.
Booth went to Bones' office, even before he opened the paper, he knew it was for him, he couldn't explain how he knew it, he just did. His hand was shaking as if he was having a seizure when he unfolded it, his mind was spinning and if he wouldn't hold onto his desire for revenge and responsibility for Parker, he would have lost his mind right there.
"Dear Agent Booth, you are a confusing man. You are irrational and impulsive, superstitious and exasperating. You believe in ghosts and angels, and maybe even Santa Claus, and because of you, I've started to see the universe differently. How is it possible that simply looking into your fine face gives me so much joy? Why does it make me so happy that every time I try to sneak a peek at you, you're already looking at me? Like you, it makes no sense. And like you, it feels right.If I ever get out of here, I will find a time and a place to tell youthat you make my life messy and confusing and unfocused and irrational and wonderful."
It's been three years and Booth finally got her. Heather Taffet, a woman that took his life away, who ruined his career. After Hodgins and Bones' death, his rage was so immense that FBI deemed him unfit for the job, but Booth didn't stop. He was looking and looking, he made it his life mission to avenge Bones and that thing that should have happened between them. When he got her, he didn't flinch, he didn't think twice, he shot her right here and there. Naturally, Booth got arrested, but he didn't care. He had nothing left in his life anyway, Rebecca was terrified of him and wouldn't let him see Parker anymore, furthermore, they moved to England to start a new life and Booth knew that most likely he would never see his son again. Cam and Zack were still working at Jeffersonian, but they moved on eventually, with their work and their lives. Cam was trying to help him at first, but he pushed her away. The only person who shared his idea of pursuit was Angela, but when Booth became dangerous, she refused to help him anymore, she wanted justice, Booth craved revenge.
Angela visited him in prison, though, they talked and she promised to do everything to help him to get out there, even though it was a pipe dream. Booth's state of mind was getting worse, he knew that, he knew something was wrong. He was seeing things, his old buddy Ted Parker, who died a long time ago, he was seeing ghosts of his father who would look at him with the same terrifying expression as it was during his childhood. He would see Bones, young and beautiful and smiling warmly at him, she used to come to his dreams all the time at first, but now she was part of his visions, hallucinations or whatever it was happening to him.
He knew he probably lost it, but he still couldn't care. His trial was short and uneventful, they give him fifteen years given the circumstances and the fact that Cam, Angela and Zack managed the impossible and proved that Heather Taffet was indeed a Gravedigger. They came to say goodbye to him and deep down he knew it was the last time he would ever see them.
A few months later Cam was in her office reading the autopsy report from the prison coroner, Seeley Booth passed away five days ago in his prison cell due to the complications from his brain tumor. A few of his personal artifacts were sent alongside with the report, his gambling chip, a picture of Parker and a Bible with Brennan's note inside. Cam volunteered to organize the memorial service, knowing exactly where her friend would want to be buried. When the funeral was over, Zack, Angela and Cam were staring at the gravestones of their two friends, who should have lived long lives, they should have saved countless people and dive into something amazing that was meant to be for them. Instead there was nothing left, but cold stones with their names on it, Temperance Brennan and Seeley Booth, reunited at last.