Hodgins, Angela, and Booth survive the explosion in the Jeffersonian lab but can’t find Brennan. Both entrances to the Jeffersonian have collapsed and rescuers can’t get inside.

Booth finds Brennan but she’s unconscious. She wakes up but insists that something is wrong with her. She wrote herself notes about Kovac but now she can’t remember what they mean. Booth is worried that she’s suffered head trauma and could have a brain bleed. 

A neurological examination shows Brennan has suffered a contusion to her brain that has compromised her ability to process complex information, but she insists on going back to work to find Kovac. Unfortunately, the explosion destroyed much of the Bone Room, leaving bones scattered and mixed in a huge pile that must be sorted. Brennan finds that she is unable to help her team as she can no longer decipher what the bones mean.

Brennan worries that she will never be the same and she doesn’t know who she is without her intellect. Booth reminds her how special she is to him and that he wants to spend the rest of his life with her, no matter what. 

The cell phone the FBI thought was Kovac’s was a decoy. He’s escaped once again. 

Angela looks over photos from Cam’s wedding and sees one of the waiters with her purse, Kovac’s accomplice, Kyle Capone but he didn’t set the bomb. Hodgins and Cam get DNA from the bomb and it’s a partial match to Kovac. Booth figures out that Kovac’s wife isn’t his wife at all but actually his sister, and his accomplice. 

The team figure out that the man Kovac escaped with was connected with rural property in West Virginia. They find Kovac there. During a fire fight, Booth injures his hand and can’t shoot. Brennan is able to diagnosis his injury and correct it, allowing Booth to shoot Kovac in the head and kill him. 

Brennan begins to recover from her brain injury. 

Aubrey is offered the same promotion but in Washington D.C. He decides to take it instead of moving to Los Angeles. Karen brings him two buckets of fried chicken to help him deal with his breakup from Jessica. Aubrey offers to share it with Karen, who accepts. 

Everyone at the Jeffersonian must pack up there things, as reconstruction of the facility begins. Angela finds the Nigel Murray memorial plaque. Brennan finds her clock which stopped at 4:47pm, the time of the explosion. She says she’s going to put it up in her new office. Booth asks why she’d want to remember the moment everything almost ended. Brennan tells him it’s because it didn’t. 

Angela and Hodgins have been working together on a children’s book.

Cam and Arastoo aren’t going to Europe for six months, but are going to Mississippi to adopt three brothers who are in foster care. While Cam is on leave, Hodgins is named Interim Director of the Lab. He is thrilled as he will finally, officially be the King of the Lab!