"The End in the Beginning" is episode twenty-six of season four of Bones, the forensic drama television series loosely based on the novels and life of anthropologist Kathy Reichs, and the season finale. This episode seems to be set in an entire alternate reality, where the people are the same but different.
The Tumour in the Brain
In the previous episode, "The Critic in the Cabernet", Brennan had become concerned when Booth admitted he was seeing things that weren't there - again. In this case Stewie from Family Guy. Someone who was not only there but is also fictional. So Brennan took Booth to the hospital and it was discovered he had a, usually benign, brain tumour. He was going to be operated on anyway.
Brennan and Booth - Together at Last?
This episode, however, opens with Hodgins narrating as a woman comes home and gets into bed with a man. The woman is Brennan, the man Booth. It looks like they have got together. Then, in the morning, there's a knock on their door and it's Cam and Jared. Only it's actually Detectives Saroyan and Booth. Apparently there's been a murder at Booth's nightclub!
Booth Has a Nightclub?
Booth - and Brennan is his wife - has a nightclub called 'The Lab'. The staff there are all familiar faces - including Zack (there's a reference to him being the type of person who would go to jail for a murder he didn't commit - which he has; in "The Perfect Pieces in the Purple Pond" Zack told Sweets that he admitted to a murder he hadn't committed so he would be institutionalised for mental problems rather than go to jail) - but they don't have their traditional competencies or roles. Fisher is a chef and Angela a hostess with poor visual imagination, for example, and Caroline is the nightclub's legal representative. Max is a shady politician. Hodgins doesn't work at the club; instead, he's a successful crime novelist. Clark doesn't work there either, he's a rapper with a gangster brother.
Brennan is a Suspect?
Brennan is one of the suspects, especially as she should have been able to hear the murder from where she was supposed to be in the club, and Cam suggests that she wasn't there and hints that she might have been cheating on her husband - and it seems that Jared quite fancies Brennan as well. Although it seems that the gun may have been silenced and Jared is suggesting that Booth is actually the killer. Only Hodgins seems to recognise the dead man. They still need to find out why the man was killed and who did it. The staff of the nightclub are not cooperating with the police to protect Brennan and Booth.
It's All a Bit Weird
This is all getting pretty surreal. Given that Booth has been seeing things, there's a definite suspicion that this whole case is connected to his health problems.