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Booth clairified their relationship as professional only, though people often assumed they did have a sexual relationship.
The other "squints" think there is something between them by hearing their strange conversation.
In the end, Booth looks at Brennan and smiles, and Brennan smiles back.
Agent Sullivan invites Brennan out on a date and asks Seeley for advice.
Brennan only uses facts to continue a case, so much so that she will state when someone hypothesizes in the lab.
In the episode, "The Parts in the Sum of the Whole", Bones said that she did not want to be in a relationship because she did not know how to change herself and that she did not have the open heart that Booth did.
This habit actually led at one point to Brennan seeing Booth naked; she broke into his house using a hidden key and walked into his bathroom, without knocking, while Booth was in the tub reading a comic book.
While talking to him she unwittingly insulted him as she usually does making him stand up in anger exposing himself to her, despite Brennan's usual cold, logical almost emotionless approach to sexuality she appeared to be slightly flustered in this instance.
He is known to be fiercely protective of both Brennan and his partnership with her.
Brennan puts her hand on Booth's arm whilst he's telling her one of his biggest secrets and he puts his hand on hers and strokes it.
Seeley is extremely impressed when he sees Brennan in a somewhat revealing dress he picked out for her, and slaps her butt later in the episode to convince others they are a couple while undercover as a street fighter, Tony, and his "sugar mama" Roxie.
In the end, when Booth is looking around for any evidence of where Brennan and Hodgins are buried, Brennan sets of a mini blast that only Booth sees.
Booth sets off running for her, and jumps in the sand, digging for her, and eventually pulls her out.