Universe 1 (October 2009)
The year had been eventful in the personal lives of Booth and Bones. In the spring, they were in a session with Dr Lance Sweets, an FBI psychologist, who off and on called them in to evaluate their partnership. He was having them play a word association game (which they hated), and in the middle of the game, Bones announced she wanted to have a baby. In the past, she had told Booth several times that she had no intention of, as she referred to it, "procreating". But the idea just popped into her head as they were throwing words back and forth, and she decided that she really wanted to do it. Her first inkling was to ask Booth if she could have his sperm. Booth was flummoxed by her snap decision and had some hesitation. Over the next few days she considered other options, but he knew that if she was going to have a child on her own, that he didn't want anyone but him to be the father.
So he went to the fertility clinic to make his "deposit" and while in the room, he had hallucinations of a cartoon character chiding him over whether he could let her raise his child on her own. A few days later he had another similar hallucination while he was with Bones, and she insisted on taking him to the hospital. The doctors found that he had a brain tumor, and it was her quick evaluation of his symptoms that made the surgery much less dangerous than if he had ignored his symptoms.
But there was a complication due to a reaction to the anesthesia, and Booth was in a coma for four days. Bones stayed by his side and worked on her new book, and it seems that she was reading it aloud to him. When he came out of the coma, he realized that he had a dream that felt very real to him, but his dream was a version of the book Bones was writing. In his dream, he and Bones were married and they were the owners of a nightclub. A lot of their friends and family were part of the dream, but the main gist was that they were very much in love, and just before he awoke, they were both thrilled to find out that she was pregnant.
It took him a few days to separate real life from his coma dream, and he spent the next six weeks recovering from his surgery. Once she knew he was on the road to recovery, Bones decided to take advantage of the downtime and went to Guatemala to assist on a dig. The day she returned home was the same day that he was released to go back to work. Bones at first thought that he was back to his old self, but she soon realized that Booth was a little concerned about whether he had lost some of his abilities after the brain surgery. Over the next couple of weeks, with her help, he seemed to regain his footing.
But there was one change in Booth that didn't go away. While recovering from the surgery, he fixated on his coma dream, and every morning when he woke up alone in his bed, he had to remind himself that he wasn't married to Bones. They didn't own a nightclub. But what became pretty clear to him was the realization that he was in love with her. He had a lot of downtime over those six weeks of recovery and he did a lot of internal examination. He realized that he fell for her the moment he first saw her in the lecture hall at American University. But after the disastrous ending of their short lived partnership, he wanted nothing to do with her and her scientific brain. However, over the next year, he just couldn't get that confounding brain, and the beautiful woman wrapped around it, out of his brain. When he finally found the perfect excuse to entice her onto a case, he jumped at it. Over the last four years, she had, in more or less equal parts, baffled him and astounded him. And he had stopped counting the number of times he had to restrain himself from closing the gap and kissing her senseless. And then, God help him, slam her against a door and make mad, passionate love to her.
But, lucky for him, he had restrained himself. He had come to know her quite well over these four years, and he knew that you couldn't rush her into anything. If he made the wrong move, he could lose her. And keeping her close was more important to him than stepping into that void, not knowing if she would step in with him. He had thought that these feelings were just an intense physical attraction, but now he realized that, week by week, month by month, it had morphed into an intense love. And when he looked all the way back to the beginning, he realized that, deep down, he knew exactly where it was heading. Seconds before their first kiss, he had said to her, "I think this is going somewhere." He had forgotten those prophetic words.
He went to his friend Cam for advice. As he stumbled with his words trying to find a way to broach the subject, she gave him a knowing look. "You're in love with Doctor Brennan". He was shocked. Was it that plain to everyone? As he found out over the next few months, it was plain to everyone - except Bones herself. So, he decided to play his cards close to the vest and try inching his way forward. She didn't believe in love. Or marriage. Or forever. He decided to work on deepening their friendship, and showing her, every chance he got, that committing to another person could be fulfilling.
They had been back to work for a few weeks when they were given a case where human remains were found along a rail line. Bones found enough of the bones to begin the investigation and sent one of her interns out to comb the area for more. An analysis of the bones showed that the person had no bone markers indicating modern life, but that he grew up in the mid Atlantic states. That led them to Amish country and the parents of a boy who had disappeared during his Rumspringa, a time when Amish young people live for awhile in a non-Amish community to decide if they will make a lifetime commitment to their parents' way of life. The boy had died in a tragic accident in a robbery gone wrong, and the FBI was able to apprehend the perpetrator and give the parents a measure of closure.