Speaking to Entertainment Weekly, Nathan acknowledged that some fans are frustrated about the introduction of Hannah (Katheryn Winnick) because it means that Brennan (Emily Deschanel) and Booth (David Boreanaz) are not together.
"I think it's the difficulties and the dissatisfaction that propels the show forward in a way," he said. "That there's some frustration with these characters that we've grown to love over five and a half years - we want them to do certain things... But obviously, if they did right away, fans would be very disappointed."
Nathan added that he is pleased with the relationship between Booth and Hannah.
"They've become actual real friends, so no matter how difficult it is for Brennan to see Booth and Hannah together, she doesn't hold it against Hannah," he said. "Her tremendously rational and logical mind tells her that this is not Hannah's fault and that she likes Hannah. She would do the same thing. So their relationship is a very healthy and very mature relationship between two very strong women."
He continued: "The honesty that has grown in this threesome has provided us with an interesting dynamic because they behave in a way that isn't expected. You expect there to be some jealousy, but there really isn't. Hannah's only jealous of Booth's professional relationship with Brennan because they get to do all this kind of dangerous stuff that Hannah misses from being a war correspondent. All of that is growing to an ultimate shift in the series."
Bones continues on Thursdays at 8/7c on Fox.