It seems fitting that for much of the Bones series finale, there were just bones everywhere.
Every episode of the show, of course, has a lot of bones, since it's called Bones, but thanks to the lab exploding, the series finale saw Bones (Emily Deschanel) wading through thousands of bones, all mixed up and all over the place. There were just so many bones.
And for a while, Bones herself had no idea what to do with them. At the end of last week's episode, we saw the team discovering that the Jeffersonian was filled with multiple explosives, right before the entire thing exploded, with Booth (David Boreanaz), Bones, pregnant Angela (Michaela Conlin), and Hodgins (T.J. Thyne) all trapped in the lab.
If they hadn't deactivated the one bomb right under the lab, they would have died, but thankfully they all lived. Bones did suffer an injury, however, and temporarily lost the connection between the two sides of her brain. She remembered all the information, but had no idea what to do with it. She knew what the bones were called, but had no idea what any of the bones meant, meaning Bones was without her biggest superpower.
So while Bones had already figured out, thanks to some bones, how to catch Kovac (the guy who killed her father and who had gone after her kids), she couldn't remember it, and it was up to her team to look at the bones and think like Bones to figure it out.
Eventually, they did it. Apparently, Kovac had met the dead guy in prison and learned where he grew up, and apparently where he grew up, there was a place Kovac could hide once he got out of prison, so Kovac used the guy to get out and hide, and then he killed the guy. And Bones figured this out with the dead prisoner's tooth, because of course she did.
And Kovac also had some help on the outside, from someone who had to steal Cam's ID card and plant the bombs in the Jeffersonian. That someone turned out to be Kovac's wife, who was actually Kovac's sister and not his wife at all! Surprise!
The team tracked Kovac down, and engaged in a violent shoot out that involved Bones getting her brain back by necessity (Booth had a broken wrist and couldn't get to his gun) and ended with Kovac being shot and then going over a small cliff in a jeep, which then exploded. So he's pretty surely dead.
Anyway, none of that really matters, because the episode was really about saying goodbye. The explosion forced everyone to pack up all of their stuff that hadn't been exploded, which also brought up a lot of memories from the past 12 or so years, especially when remembering things was the only thing Bones' brain was good at anymore.
She started to worry that she was no longer herself, which prompted a beautiful, soul-fulfilling speech from Booth about how she was still and would always be the woman he fell in love with.
"I don't care if you know about the bones," he told her. "Or if you know how to solve crimes. All I know is that I want to spend the rest of my life with you. This is you, Temperance Brennan. You're my partner. Don't forget that."
In the end, everyone was on their way to a happy ending. Or more accurately, a happy middle.
Cam (Tamara Taylor) revealed that the real reason for the leave of absence was that she and her new husband Arastoo (Pej Vahdat) were heading to Mississippi to pick up the boys they were adopting. And in the meantime, she was naming Hodgins the temporary lab director/"King of the Lab."
As for Booth and Brennan, they ended the series reminiscing about the dearly departed Sweets and how he was right about everything, and then with Bones revealing that she planned to keep the clock that stopped when the lab exploded.
"Why would you want to be reminded of the moment everything almost ended, Bones?" Booth asked.
"Because it didn't," she said, which is really the truth. The show may have ended tonight, but nothing else did. And while that's not as exciting as everyone dying or watching the world end, it's nice for these characters who have been through so much and lost too many people. Here's hoping whatever comes next for them involves a lot less shooting.
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