She serves as a temporary replacement for Booth in "The Fire in the Ice" when Booth is the prime suspect in the murder of the victim (with whom Booth had fought previously after the victim played roughly in a hockey game). While she is interrogating Booth, the two flirt, and Agent Perotta appears to have a crush on him from then on (even asking Brennan if Booth "twinkles his eyes at everyone," since he did so with her). However, she never really connects with the squints- to the extent that Jack Hodgins and Wendell Bray automatically correct her description of them as 'her people' to inform her that they are Booth's people- and at the end of the episode, it is implied when Booth is ice skating with Brennan that he is past the attraction.
In her second appearance in "The Hero in the Hold," she appears at a few of the crime scenes; however, due to the fact that the team, while working to find Booth (who was kidnapped by the Grave Digger), bends some FBI protocol to do so, Perotta is somewhat pitted against the squints.
Perotta is once again a temporary replacement for Booth after he becomes incapacitated due to back problems in "The Princess and the Pear;" in fact, it is revealed Brennan actually requested to work with Perotta (although Brennan states that this was because working with someone familiar is more advantageous than working with someone new, rather than personal attachment to her). The two manage work fairly well together and solve the case. At the end of the episode, Perotta goes to visit Booth to deliver some of her homemade chili (implying that she still has feelings for him), only to find him and Brennan in a rather awkward position (Brennan is in the process of fixing Booth's back). Embarrassed, both she and Brennan leave, much to Booth's chagrin.
Part in the ShowEdit
Perotta shows an almost instant attraction to Booth when interrogating him in "The Fire in the Ice." Booth appears to be a bit more experienced as an FBI agent than Perotta, leading to an admiration of him as well as a crush.
In "The Princess and the Pear," the car that Brennan and Sweets are driving is run off the road by the murderer; when Booth finds out about this, he tells Perotta not to let Brennan go out into the field alone, and then adds "If anything happens to her...that silky black hair, that soft skin..." (being under the influence of Vicodin, his back medicine, at the time). After telling Brennan that she is not to go into the field alone, Brennan states, "Booth can be needlessly protective sometimes; I have no idea why," to which Perotta responds with, "You really don't, do you?", implying that she senses the sexual tension in Booth's and Brennan's relationship.
Still, despite her jealousy of this relationship, and hints at an underlying rivalry between Brennan and Perotta, the two appear to work quite well together.