"People were broken apart [in the finale] and we're going to try to see how they come back together... if they come back together," Nathan explained.
"Booth and Brennan have a lot to deal with. She might've done the right thing, but she broke up the family [and] went away. She took his daughter. And they're going to have to get past that."
David Boreanaz (Booth) recently hinted that his character will "have to re-examine" his romance with Brennan, following the events of the last season.
"I think that time heals a lot," he speculated. "I think that he'll have to re-examine the relationship, re-examine where the two of them are. He'll play it out from there and see where they are and where it takes them."
Bones returns to Fox on September 17. In the UK, the series airs on Sky Living.