Stephen Nathan told TV Guide that it will be the FBI agent's own issues that cause problems in his relationship with war correspondent Hannah Burley (Katheryn Winnick).
"[Booth] has forged a new life for himself emotionally," he said.. "Of course, all of this occurred when he was not around Brennan (Emily Deschanel). So Brennan's presence in the mix will alter the relationship. It just has to."
Nathan also hinted that Booth may not have entirely moved past his feelings for Brennan.
He teased: "He's moved on, but whether he continues to move on is another thing entirely."
Emily Deschanel recently admitted that it had felt "weird" filming scenes with the new love interest.
Bones returns to Fox on September 23.