She had intercourse with Zack a month prior to the events in A Boy in the Tree, but she hasn't returned a single call ever since because she thought that Zack failed to perform sexually. Throughout the episode, Zack has been asking everyone for help with his relationship with her, but almost everyone refused to help, especially Booth. In the end at Wong Fu's, Angela gave him some advice to help win her back; telling Naomi that he doesn't know anything about "lovemaking" and let her teach him all the secrets of love to leave them at a blank slate.
Zack apparently took Angela's advice since he mentioned that Naomi wants to be the front half of a cow for the Jeffersonian Halloween Party in Mummy in the Maze while Zack is the back half. She is seen going to the Halloween party alone while Zack, Hodgins, and Brennan search for Megan Shaw before she is murdered by Pete Geller.
Because of Zack's role in the rampage of Gormogon, their relationship is most likely terminated.