Six months after the events of last season, Booth, Brennan, daughter Christine and the new baby are seemingly living a dream life, a world away from the murder-filled life they left behind. But a case with close personal ties to the couple forces Brennan to become involved in the forensic analysis of the remains, and Booth mysteriously goes missing, prompting an FBI investigation into his whereabouts led by Agent Grace Miller (guest star Kim Raver), who works closely with FBI Agent James Aubrey on the case. However, tensions rise when Miller tries to investigate one of the team’s own as the primary suspect. The case also brings Brennan into contact with a member of Booth’s family (guest star Dilshad Vadsaria), and “squintern” Arastoo Vaziri (guest star Pej Vahdat), who has been filling in as lead forensic anthropologist during Brennan’s absence, hopes the temporary position becomes permanent.
The season's premiere begins six months from last season's finale with Booth playing with his son who he says is smelly. Bones is going over ancient items, specifically a very old plow, with Christine and teaches her how to categorize them. Bones says Angela and Hodgins are bringing the kids over tonight. He says it’s a busy night but she says he needs to be there. He says he’s got to go to work and Christine says to tell Uncle Aubrey she said hi. Booth reminds her that her daddy freelances as a trainer at the FBI and isn’t part of the FBI now.
He heads out with a long look back. Hodgins tells Angela he has some fast replicating microbes and says it's the building blocks of beer. Cam comes in and says she’s been trying to find a replacement for Brennan but she keeps rejecting candidates when she consults Brennan on the possible choices. Cam says there’s one name in particular but she’s not sure. She asks about Aristoo and Hodgins says he’s perfect and is already filling in for her. Cam says she’s dating him so doesn’t want to do wrong.
Cam says they have a body in a van that’s been torched. At the scene, Hodgins says an incendiary device was used to torch the body and van. Aubrey says the van was stolen and they talk about the van being left on a remote property. Arastoo says it’s a male and he thinks white and in his 40s. Cam asks for cause of death and they talk about a gun fused to the victim’s leg and a titanium toe insert, stating how the items found on/near the body were of professional use.
They take the van back to the lab and Arastoo asks Hodgins to work faster. They lift the top of the van off without disturbing the bones. Cam says the tissue is all ash and Arastoo tells Cam she won’t get anything from the body. Angela arrives and says she ran the serial number on the gun and is in utter shock – Cam asks who the gun belongs to and Angela says Booth’s. Cam and Aubrey come to the house to tell Brennan the news.
Bones says he’s at work and is just running late. Cam says Arastoo said the skeletal features match Booth and Aubrey says the gun is Booth’s. Brennan says he doesn’t carry his gun and she opens his gun case. All of his weapons are gone and he left his wedding ring behind. Bones rushes to the Jeffersonian and asks Arastoo what he’s found so far. She says it’s up to her and Angela says she shouldn’t look at the remains. Brennan says she’s the most qualified and talks about damages from parachute training.
Arastoo says the bones have the remodeling she mentioned. She looks at ribs and she says he was beaten as a child and has defensive fractures. Arastoo says those are there too. She asks about his brain surgery and he says the brain was too destroyed. Brennan says to leave her with the bones and Cam tells Arastoo it’s okay. Angela asks if she thinks it’s him and Brennan says it can’t be him – they left this all behind. She’s in denial and looks scared.
Later, she has the bones cleaned and laid out on her light table. She stares at them for a long time then starts a closer examination. She holds his skull in her hand and thinks about early in their relationship the first time they kissed. She touches his fingers and thinks about him holding her had. She thinks about when he was shot and she held her hand to his chest to stop the blood from flowing out. Aubrey and Caroline have a room full of agents assembled to work Booth’s murder case.
Caroline says to use your anger to help solve this and says there’s no time to waste. Caroline tells Aubrey that Booth was in his office for a decade. They wonder why Booth had a gun and Caroline wonders why he didn’t bring the problem to them. Angela does a reconstruction on the skull. It looks like Booth – Hodgins agrees. Angela wonders why Booth would put himself in harm’s way. Brennan comes in and says it’s not him.
She says she has proof. They follow her to the light table. She tells them he was in a firefight a year ago. She says a bullet passed through a portion of the rib bone. She says the bullet exited and took out a small part of the left scapula. They all agree that Booth is alive. She tells Cam she hopes this is not how she’s running the Jeffersonian without them. Brennan yells at them and says they have to figure out who this is and says Arastoo told her that her husband was dead.
She says whoever this is had Booth’s gun and she’s not leaving until they find out. Aubrey and Caroline go to work with this new information. They show Booth accessed the armory at Quantico. Aubrey gets a text and says he put out an APB on Booth’s car and it’s at Reagan International. But Booth never got onto a plane. Agent Miller shows up to collaborate on the case. She’s from internal investigations. Caroline says they sicced her on Booth. Miller says Booth is a suspect and Aubrey doesn’t like that.
Aubrey says if she’s making accusations they don’t need her. She says Booth is clearly a suspect. Aubrey is annoyed. Bones meets with Miller and she asks when was the last time she saw Booth and she says 8:36 am. Caroline explains she’s very precise. Miller asks her to explain his mood. Brennan says humans act in seven different ways. Brennan says emotions aren’t her area of expertise and says she’s deliberately making her uncomfortable to try and extract something.
Bones says she’s not comfortable talking to her. Miller says she’s the suspect’s wife and Bones says she can’t solve the case without her. Caroline tells Brennan to tread lightly and says Booth’s life might depend on it. Arastoo comes to see Hodgins who has some buffelgrass and he says it germinates after high heat. Arastoo asks him to look at this vertebrae. They see osteoblasts and Hodgins says the person was an alcoholic. Arastoo says Brennan found it and that’s two things he missed.
Arastoo shows Hodgins a ring and says he wants to propose to Cam but he feels inadequate over this. Hodgins says he’s not Brennan but he’s good and Cam knows it. He tells him to take his shot. Angela goes through Booth’s phone records and tells Aubrey there was nothing out of the ordinary. Angela says they’re doing this the wrong way and says they need to look at who he didn’t talk to. He ignored calls from some numbers and Aubrey says one is a code. The message is “GO” based on the number of rings.
Looks like whatever it is, Booth wasn’t working alone. Arastoo shows Brennan a wound he found – it’s cause of death from a gunshot. Then Bones shows him some remodeling and Arastoo says it’s from a scalpel. Bones says she knows who this is and they wonder if it’s Jared – Booth’s brother. Bones says they have similar childhood injuries and they look a lot alike. Bones says she’s sure it’s Jared Booth.
Brennan is with Miller and tells her that Jared married Padma eight years ago but it didn’t last. Miller says she knows the wife was a hooker. Bones says Jared bounced around a lot. Miller says Booth may be more like his brother but Miller spouts off facts like his gambling addiction. Brennan says Booth worked on his weaknesses and Jared did not. Miller implies Booth killed Jared and Bones says no way. Angela traced the phone that sent the Go message. 14 phones were bought together.
Five were activated at a time. Aubrey says it’s a team, not just Booth and Jared. Cam wonders what the Booth brothers were involved in. Padma tells them that Jared owed money but not something that would get him killed. Miller points out expensive gifts and Padma says Jared was trying to get back with her. She says a friend of Jared’s was trying to get him back on track. She shows them a photo and points out Kevin O’Donnell. She says he was like a brother to Jared – implying that Booth was not.
Arastoo shows Cam he found post-death abrasions on the skull. There are particulates but the heat from the fire may have changed it. Cam sees the ring box and Arastoo snatches it up and says she wasn’t supposed to see it because it’s not the right time. Cam says there’s so much going on and he asks if she wants to see it. He says he’s not proposing, just showing it to her and pops the ring box. She smiles and Hodgins comes in and says he asked her. Arastoo says and Hodgins asks if she said no.
Hodgins creeps back out the door. Aubrey and Miller go to see O’Donnell who is now a school teacher living in a run-down place. He asks what it’s about and they tell him what has happened to Jared. He says Jared was in his unit and they were tight. They ask when he saw him last and he says two nights ago and Jared was supposed to meet him last night. He says he had a job and was making good money working security somewhere. Kevin says Jared went through hell and says he’s a hero and he resents Miller making garbage assumptions.
She says she has a few more questions and he tells them no more and kicks them out. Aubrey offers his card. Kevin won’t take it so he leaves it on the table. Kevin slams the door after them. Brennan comes into her old office at the Jeffersonian. Angela comes in and says she found pudding cups for them. They eat and Bones says she knows food is a standard offering for grief but says there’s no evidence Booth is dead and says he’s still out there. Angela says she hopes so.
We see Booth lying with a gut shot in a warehouse somewhere and he looks bad. Arastoo tells Brennan he sees symmetry in some of the wounds. They agree it was a blow from something large. He says maybe a fall and he says maybe Jared was trying to stop his own fall. She sees impact fractures and they conclude he must have fallen about three stories. Bones says the glass may be from where he fell. Hodgins says it’s lead-based glass and only made in Turkey.
Arastoo says if he was shot through the window he could have fallen. Miller shows Caroline and Aubrey financial records of Jared and says Booth opened a bank account and sent it to Jared. Aubrey asks why Miller is so intent on ruining Booth’s good name. The squints get on a video conference with the three FBI personnels. Angela says they narrowed the grass seed location and then they cross-checked with lead-based glass. Miller mocks their efforts.
They tell her it’s McLean, Virginia and Caroline says it’s Victor Masbourian’s house. Aubrey says Booth might be held captive there. Miller loads up a SWAT team to infiltrate Masbourian’s place. They come in hot, ready for anything, armed to the gills. They drill out the lock and move in silently. There don’t seem to be any lights on. They spread out through the large house and clear it room by room. Miller and Aubrey are together. They head upstairs.
They head into an office and find bodies and blood. Aubrey calls down and says it’s a blood bath. Masbourian is dead and Booth isn’t there. They call in crime scene techs and the squints roll in. Cam says Masbourian was killed 28 hours ago, six hours after Booth was last seen. Aubrey says they have no proof that Booth was there when Miller says Booth likely did this. Hodgins found a wall safe and says it looks vintage. Hodgins says it was wired and opening it tripped a silent alarm.
Miller says this was a robbery and Booth is one of the culprits. Brennan stares at the bones on her table and Arastoo says there are three bodies on the way. She tells him to get some sleep and he asks how she’s holding up. She says she’s angry and has more questions than she’s used to. She says Booth promised he wouldn’t see Jared but Arastoo says there’s a bond between brothers that can’t be turned off. Brennan says she and Booth discussed this many times and he kept this from her.
Caroline is at the office late waiting on Aubrey. She says she did some digging and says she looked into Miller who has been holding out on them. She says Booth isn’t the only agent missing – Miller’s partner is missing too but it’s not on the wire yet. Aubrey wonders why Miller didn’t tell them and Caroline says to find out. Hodgins says the safe was stuffed full of currency – likely hundred dollar bills. He says it was $2 million. Cam found proof that Booth was there – it’s DNA. Angela says it was a five man team at the drug dealer’s house. Cam comes in and tells Brennan she found Booth’s blood at the scene. Angela has set up a simulation and Cam says Booth sustained a major wound and he needs medical attention now. We see Booth washing his stomach wound and a guy knocks on the door and asks if he’s okay. He says he’ll be right out. The other guy says he looks bad but Booth says it’s just a scratch. Kevin is there and the other guy says Booth needs a doctor. Kevin says no doctors. He asks if Booth is still with them and he says yes.
- Temperance Brennan - Emily Deschanel
- Seeley Booth - David Boreanaz
- Jack Hodgins - T.J Thyne
- Angela Montenegro - Michaela Conlin
- Camille Saroyan - Tamara Taylor
- James Aubrey - John Boyd
Intern of the WeekEdit
- Patricia Belcher as Caroline Julian
- Sunnie Pelant as Christine Booth
- Dilshad Vadsaria as Padme Dalaj
- Kim Raver as FBI Agent Grace Miller