By Mandi Bierly
Updated May 14, 2012 at 12:00 PM EDT

Spoiler alert! If you haven’t watched the season finale of Bones, stop reading now. The return of Christopher Pelant (Andrew Leeds) produced a twist you won’t see coming. (Update: Read our postmortem interview with creator Hart Hanson.)

Bones is a show that enjoys being goofy, but it takes its finales seriously. There wasn’t much laughter at all in this hour as Pelant framed Brennan for the murder of Ethan, a brilliant doctor/mathematician with whom she’d secretly been consulting on the Pelant case at the mental institution where Ethan was a patient. Ethan thought Christine was a demon and threatened to kill her, so that was supposed to be hyper-rational, wonderful mother Brennan’s motive. Through a computer glitch, Ethan had been moved to a minimum security area where he wandered off. It turns out he had been sedated with some kind of toxin distilled from a rare plant that Hodgins had two of — until two weeks ago, when Brennan asked him to borrow one because she said she was studying a tribe in western Colombia that used it for the tip of their poison arrows. Ethan had been cut near minor arteries so the scent of blood would attract wolves that would think he was dead since he wasn’t moving and devour him alive. Pelant had no background in anatomy, but of course, Brennan did.

Seeley received a call from Brennan saying Pelant had her at his place, and he went charging in and beat the crap out of him. I normally love seeing protective Seeley come out, but having guessed from Brennan’s stilted voice on the call that it was a fake — Pelant had already changed their ringtones to howling wolves — Seeley’s rage was frustrating to watch because you knew what was going to happen. Seeley putting Pelant’s head through a window and kicking him when he was down was all Pelant’s lawyer needed to win him parole and get Seeley and Brennan thrown off the case. Sweets got taken off it when he kept saying his profile fit Pelant instead of Brennan. Angela was pissed at Cam for reporting all the damning evidence to the new agent in charge, but after Caroline got tossed off the case because Pelant made their bank accounts look like Brennan had paid her off (I guess to put the wrong address on the search warrant to buy Brennan some time), she told Angela that Cam was the hero — she was the only one who hadn’t done what Pelant expected. She was doing everything by the book so the Jeffersonian would still have access to the case. It was particularly tough on Cam to report that hair found in Brennan’s car trunk matched Ethan. Excellent crying by Tamara Taylor.

With the evidence mounting against Brennan, Max wanted her to run — but Booth said it would only make her look more guilty. Angela hacked into Pelant’s life and discovered he’d been borrowing an insane amount of books from the library, along with ordering tons of movies on pay-per-view. I guess the thinking was he couldn’t possibly be reading all the books if he was watching that many films. Angela got all the books, but couldn’t understand what he was doing with them. Finally, Brennan remembered that Ethan had signed the book he’d given her the last time she visited him — he was trying to send her a mathematic message. It was an Alexander Pope quote: “Nature and nature’s laws/ Lay hid in night/ God said “Let Newton be”/ and all was light.” Since Booth and Brennan couldn’t go into Ethan’s room, Hodgins and Cam had to do it. They used the blue light to find where Ethan had written some kind of code in a giant triangle that nearly took up one wall. He’d written it in his own saliva — thank god it wasn’t another bodily fluid. (Not really Bones‘ speed, I know, but it’s May Sweeps! I know I wasn’t the only one worried.) Angela figured out that books and computer codes cross when the library scans the books. Each book has its own code — so Pelant must have been putting whatever code he created for a particular devious act on a book, and when it was scanned, it would upload his directive like a virus. I have no clue if any of this is possible, so let’s just assume it is. Angela told Caroline about the book viruses, but Caroline had already been thrown off the case. This seems like a solid lead though, right, that the FBI should want to investigate? Or, should we assume that there’s no way to trace the “virus” back to the code on the books? I’ll get a headache if I keep thinking about this.

Brennan agreed to go to Christine’s christening, and I suppose I wanted to think it was because even if she didn’t believe in religion, she believed in spending time together as a family before she turned herself in ahead of the arrest warrant. But it was just so when Booth went to get the car (that wouldn’t start, thanks to Max), Brennan could speed away with Christine in a second car Max provided. I only figured that out when Brennan told Booth that she wanted him to know she loved him — they weren’t just together because of the baby. That sounded like something you say before YOU KIDNAP A CHILD and go on the run to meet up with your fugitive dad later. Seeley handled this better than I thought he would. He didn’t punch Max, even though he probably wanted to. I suppose that means deep down he knows Max is right: Brennan was going to be arrested, and once she was in the system, Pelant could orchestrate whatever fate he wanted. Max knows how to live as a fugitive and he’ll keep her and Christine safe. Max wants Seeley to stay in the system so he can prove her innocence and bring her home.

While Christine was getting christened, Pelant walked right into Booth and Brennan’s house and switched out their alarm clock, which read 4:47, naturally. I’m thinking it could be a bomb that will go off when the alarm rings. Too dark? Maybe just a wire so he can hear the conversation in the bedroom? A camera? What was up with him being on camera? Was that just their own nanny cam, or was it a feed to his computer as well? What did he take a Polaroid of in Christine’s area and why? I hope this is all supposed to be as big of a mystery as I’m making it…

We know producers spent a lot of time agonizing over what the final shot of the hour should be. It was of Brennan’s car driving in the night. They can’t keep her away that long, right? You don’t want to squander the chance to milk a juicy story, but you also don’t want people who tune into a show for the chemistry to not see it. (Though I would love seeing badass Max in the picture again for a couple episodes because it would feel like classic Bones — some of my favorite episodes involved Brennan’s family backstory — and also mean Ryan O’Neal is doing well.)

I guess there was some humor after all: Booth and Brennan finally get together, and now they’re physically apart. Everyone was worried Brennan wouldn’t be an affectionate mother, and now it’s her love for her child that’s being used against her. (Though wouldn’t hyper-rational Brennan also know she’d be a suspect and be smart enough to get the hair out of her trunk?)

Read more: