Season 5 Episode 1 'Harbingers in the Fountain' after Bones got stabbed in the arm by the doctor.
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Bone of ContentionOpinions by our Answers.com contributors:In the second-last episode of season 4 ("The Critic in the Cabernet") Bones decides that she wants to have a baby - but without any emotional ties. She asks Booth to be the father. Booth agrees because he wants her to be happy. During the course of the episode, Booth starts seeing hallucinations of Stewie from "Family Guy," who tells him that it is not like him to just leave Brennan to have the baby alone without being attached in any way. Near the end Booth breaks down, telling Bones that he can't not be involved with his own child. She tells him it's fine, that she won't have a baby. Booth is relieved but not for long: After telling Brennan about seeing Stewie, she tells him something is not right and takes him to the hospital. It turns out that he has a brain tumor and needs to be operated on right away. Before going into the operating room, he tells Brennan that if he doesn't make it, he wants her to have his baby.The last episode ("The End in the Beginning") starts with Booth and Brennan. They are married and own a nightclub. Hodgens is a famous author, Sweets is a singing bartender, Fisher is a chef, Angela is the door woman and Cam and Jarred (Booth's brother) are FBI. (Zack is also back). At the end of the dream, Bones tells Booth that she is pregnant. When the dream fades out, we find out that the whole episode was Booth having a dream (while in a 4-day coma) based on what Bones read him from her latest book. When Booth wakes up, he asks her who she is. What he really means, though, is which Brennan she is.So, to answer your question: No, Bones is not pregnant with Booth.In the above episode, Bones is not pregnant with Booth's baby. However, in "The Hole in the Heart" it is shown that Bones slept with Booth after Vincent's death. In the next episode ("The Change in the Game"), Bones announces at the very end of the episode (after Angela gives birth) that she is pregnant and that Booth is the father. They smile at each other. So, yes, Bones is pregnant with Booth's baby.
No and yes
In the season finale of season 6. "the change in the game".
Spoiler alert for episode 3x09 They kiss beneath the mistletoe as a deal with Caroline, the Lawyer, in episode 3x09, The Santa in the Slush. Spoiler alert for episodes 6x22 and 6x23 They don't kiss again until episode 6x22, The Hole in the Heart, when they fall into bed and are understood to have sleep together after Brennan admits that she is pregnant with Booth's baby, in the next episode, 6x23, The Change in the Game.
No, Booth and Dr. Brennan are not married. In the last episode of season 4 of the show, they were a married couple expecting a baby but that was just a dream that Booth had while in a coma.