When Bones returns with new episodes on September 17, Booth may utter those magical three words to his partner, but that doesn't mean everything is back to normal for this pair.
According to series creator Hart Hanson, Brennan's baby-making dreams were crushed this past May. Referring to her plans to get knocked up by Booth, Hanson told Michael Ausiello:
“She does not want to have his baby if he doesn’t want her to have the baby. It was really significant that once he had doubts, she wasn’t like, ‘Oh, I’ll have the baby with someone else.’ If Brennan wants to have a baby, she wants to have Booth’s baby. Her interest in having a child declines to zero when she considers having anyone else’s baby.”
That's sweet. And sad.