Plot hole: In the beginning of the episode Booth is brought in by ambulances because he was shot. The episode flashes back and follows back through the events leading up to that. At the end of the episode he is arrested and accused of murdering 3 FBI agents who were coming "to serve warrants." In actuality Delta Operatives had tried to kill Booth. If Booth had been picked up at the scene of the battle by paramedics, the medics would have seen the dead bodies of the operatives in their gear and been able to easily prove Booth didn't just murder 3 agents. Furthermore, the medics on the scene would not just ignore the destroyed house and dead bodies. They would have called local PD and Booth would again be off the hook.