First, let me say that there is a quick scene in this episode that cracked me up. This means: I put the DVD on pause just so I could laugh. Its not very realistic, but the shot is really slapstick-comedy funny. (Cp. the bounty-hunter getting the carpet pulled out from under her)
Anyway, the plot is a little different because in this episode, Bones gets to be the rescuer and Booth is the one needing to be rescued. Fine point: Bones actually reacts to the fact that Booth needs rescuing; i.e. Bones is stressed and emotive. The development with Bones' father ties this episode to many of the subplots and such of the previous episodes. There is one glaring flaw: her father keeps appearing in her apartment. Well, you'd think after he'd done it once, the FBI would be ready for his next attempt. Apparently, he is not only a criminal, but Spider-Man.
There are some other minor unrealistic scenes in this episode, which purists will dislike. (For example, Booth is really Wolverine for the beating his head takes.) However, its TV - not string-theory physics class, so accept the improbable and enjoy the entertainment.
Finally, there is a neat treat getting to hear Bones sing a verse.