Once again it wasn't so much the crime which took centre stage but character development.
Brennan and Booth are working apart on this case and Booth gets into deep trouble. The extent to which Brennan cares for him is shown in the lengths she goes to trying to find him. For a start she gets help from her father despite her ambivalent feelings about him. Towards the end her attitude is beginning to change as she becomes uncertain if she should call him in next time he appears.
The affection that the squint team have for Booth is shown in their desire to find out where he is despite Zack pointing out that they find evidence and Booth interprets it and they are no good at interpreting.
Booth takes a heck of a beating, and is tortured as well but won't reveal that Kennedy is still alive. Not surprising this as Gallagher would have killed him straight away. He doesn't point this out to Brennan but says that he had to give her time to find him.It is obvious that he was badly hurt as when they are in the diner talking, there are two crutches propped against the wall behind him.
We have here an 'honourable' ex-killer in Kennedy who is now retired and doesn't kill for fun. He even makes sure that Booth keeps his gun so he won't get into trouble. We know that Booth, despite his job, prefers upright criminals to crooked cops.
Add in a female bounty hunter, a faked death, Zack advising Booth by cellphone how to find the one legged man and you have a great episode.