Bones outdid itself in its Season 9 finale with an episode that indeed changes everything, as the producers promised, and was one of the most exciting hours in the history of the series.
Bones bursting in and saving Booth with her gun was one of the all-time best scenes in the series, period. And Booth and Bones taken into custody in the hospital was one for the books (more on that - and the government conspiracy - in a moment).
First, I'm wondering why Booth didn't even make an attempt to get some military buddies into his fight with the Delta Force commandos sent to kill him. I get completely why he didn't want Bones there, and Sweets wouldn't have lasted a minute, but surely he had some people with military prowess in the Washington area that he trusted and could call upon.
As to the FBI and the conspiracy within our government, this is indeed a new and powerful tack for the series. Hunting down brilliant serial killers, including even one who was their intern at the beginning of the series, is one thing. Fighting against our government itself is quite another, and moves Bones into Bourne Conspiracy territory. And I sadly have little trouble believing that the FBI and our government could have within it some cowards, like Booth's superior, or people engaged in much worse. As Occupy Wall Street and the police response to it demonstrated, our law enforcement all too often steps on the lawful activity of citizens.
Agatha Christie mined this theme very well in The Secret Adversary nearly a hundred years ago (1922), and it's great to see Bones go in that direction now. I'll be back here in the Fall when the premiere episode of the 10th season continues the story begun in this finale.