It’s been six months since the season 10 finale and Booth and Brennan are at home with Christine and their new baby boy. Brennan no long works for the Jeffersonian and she’s written two new books since she’s left. Booth is a freelance instructor at Quantico. When he leaves for the day, he gives his family a longing look before he walks out the door.

Aubrey calls in the team at the Jeffersonian to a body found burned in a van. Arastoo believes it is a male in his 40s. A gun, which appears to have been in an ankle holster is seared to the bones of the leg and a titanium plate is left of the high end combat boot. 

The serial number on the weapon matches Booth’s as do many of the gunshots and fractures from childhood abuse. Brennan says it can’t be her husband because he no longer carried his weapon but when she goes to get it she finds it missing and his wedding ring in its place.

Arastoo believes the body is Booth’s but Brennan disagrees. Even Angela’s reconstruction looks like Booth.  She insists on doing the examination herself. After several hours she finds one discrepancy int the bones that tells her this isn’t Booth. Arrestee is worried that he missed it. Cam is considering making him head of the lab and he has a ring and is planning to propose. Later, Cam finds the ring but before Arastoo can show it to her, Hodgins walks in and interrupts. 

Special Agent Grace Miller from Internal Investigations joins the investigation to find Booth but she irks Aubrey when she considers Booth a suspect. 

Turns out the body in the van was Booth’s brother, Jared. Jared needed money but Booth refused, but Booth was secretly in contact with Jared and didn’t tell Brennan. Jared had a burner phone that contacted four other burner phones so the team determines there was a team of five working on something. 

The leaded glass in the body leads the team to the house of a drug lord. When the FBI team gets there, the drug lord and his men are dead, and his safe is empty. From the blood splatter, they learn that Booth was injured in the fire fight. 

Agent Miller believes that Booth helped rob the drug dealer. Aubrey learns that she’s hiding that her own partner has also gone missing.

Elsewhere, Booth is injured and with a group of men counting the money, including Kevin O’Donald, Jared’s former team leader from the military who appears to be in charge of what ever is happening here.