The Hero in the Hold. Booth goes to the hospital, and they find out that he has a brain tumor and needs surgery immediately - the doctors don't want to take any risks. Right before going into surgery, Booth tells Brennan that if he doesn't make it, he wants her to have his child with his sperm donation and that she would make an excellent mother. The End in the Beginning In an alternate storyline, Brennan and Booth are married and own a nightclub called "The Lab," in which a dead body has been found.
They, along with their staff at the club most of the other cast members of the season , are suspects in the murder case, which Cam and Jared are working on. In the end Booth and Brennan go to her office to have drinks when Brennan says she can't do it anymore. In the real world, Booth wakes up from his coma and doesn't recognize Brennan.
Harbingers in the Fountain Booth has gotten his memory back, but still acts differently around Brennan. We learn that for a while he had thought Brennan was his pregnant wife, like in the dream. Angela's psychic, Avalon Harmonia, even states that Booth never lost something while he was comatose - he gained something. Soon Booth realizes that he is in love with her, admitting it to Cam.
But Sweets shows Booth scans of his brain before, during and after his coma-dream and theorizes that Booth's newfound love for Brennan is only a result of his coma, that will fade with time. Booth shows the psychic the scans, but she tells him that the doctors can scan his brain for what's inside, but they can't scan his heart for what's inside.
She makes him cut her deck of cards, and he gets the devil card indicating Brennan is in danger. Booth rushes off and saves Brennan just in time by shooting the doctor who has attacked her at a clinic.
After Bones pulls out the knife the doctor stabbed her in the arm with, Booth holds her while putting pressure on her wound and tells her "I got you. I got you baby. He then tells Brennan that he loves her - only in a "professional and atta girl kinda way.
The Bond in the Boot In the last scene of the episode, when Brennan is helping Booth fix his sink, Booth puts his hand over Brennan's and they have a moment. He puts his arm around her in order to turn the water on, despite it being easier for him to get up and do it. Beautiful Day in the Neighborhood Parker wants Booth to get a girlfriend, so he asks all of Booth's female colleagues to be his father's girlfriend - including Brennan.
But in the end, Brennan figures out that Parker only wanted Booth to have a girlfriend because his friend's father got a girlfriend and then moved to a new house with a pool - and Parker also wants a pool. Booth is visibly jealous and Angela tells Brennan that Booth wants to go out with her himself, that's why he's being difficult about the subject of her and Hacker.
Brennan misunderstands and says that she and Booth go out together all the time, but with Hacker there is the possibility for sex. Booth gets upset with Brennan when he learns she said something trivial about him to Hacker, because he's uncomfortable about her going on dates with his boss. Later, when the team attends an event at a museum and they have a moment; they stand so close, it almost seems like they're about to kiss, but then the team comes in and interrupts their intimate conversation.
Tough Man in the Tender Chicken After having a fight with Angela, Booth asks Brennan what's bothering her but refuses to help when he learns the issue, saying that if he gets involved and chooses a side they will both be angry at him when they make up.
He then says that he would die and kill for Brennan, but he's not going to get in between her and Angela. He assures her that everything will be alright with Angela though. The Dwarf in the Dirt Sweets tells Gordon Wyatt that his book about Booth and Brennan concludes that the two are in love with each other and that Brennan uses her intellect to shield herself from intense emotions - like love - because of her childhood trauma and that opening up her heart to Booth would be equal to some kind of assault for her.
Angela tells Wyatt that she thinks Booth misses the dream he had when he was in a coma. Booth realizes that he is in love with Brennan and wants the kind of life with her that he had in the dream, which is why he can no longer shoot straight. He has also changed some of his routines, such as drinking coffee and talking in his cell phone with the opposite hand than the one he used before the surgery, and stepping on a ladder with the other foot first, things that Brennan noticed.
When Wyatt presents Sweets' theory to Booth, he says that he knows Brennan doesn't love him back, that if she loved him, he would know. Wyatt tells Booth to have hope and patience, silently indicating to Booth that Brennan will eventually come around. And Wyatt says that in order to ace his marksmanship certification, he should imagine having the life with Brennan he wants, take her to the shooting test, and imagine that he has to shoot straight at the goal to protect Brennan.
The advice works, and Booth gets a perfect score on the test. The Foot in the Foreclosure When Booth's grandfather comes to live with Booth for a while, he meets Brennan and tells Booth that, "[he] wasn't kidding about this one. Later, Hank tells Booth that he can give Booth and Brennan some privacy if they need it, but Booth says there's nothing going on between them. Hank wonders how his grandson can just be friends with Brennan and forms a bond with her before he goes back to the nursing home.
When Booth and Brennan drop him off, Hank speaks to Brennan alone, saying that Booth does need someone to be with him, that she shouldn't be scared, and not to have any regrets in her life. The Goop on the Girl A man dressed as Santa stages a robbery in a bank and runs when the police arrive.
The bomb he carries underneath his clothes then explodes. Booth, who has evidence of the Santa on him, is also brought to the lab. Brennan starts to undress him, much to the amusement of Cam who walks in on them at the exact most unfortunate time.
After pursuing a suspect, Booth pins him to the ground and tells him to stay still. Brennan says, "I should warn you, he's very hard to resist. The Parts in the Sum of the Whole We go back in time to Brennan and Booth's first case, and while investigating, Brennan asks Booth if he's seeing anyone. Booth tells Brennan he'd ask her out if it wasn't prohibited for agents and consultants to be romantically involved.
After they met in a bar after hours, Booth confesses to Brennan that he has a gambling problem, and they kiss. Brennan even tells Sweets "there was tongue contact. They tell Sweets that it took a year before they could be in the same room together again. After they leave Sweets' office, Booth takes his advice and tells Brennan that he wants to give their relationship a shot and kisses her. But Brennan says no and that she doesn't have his open heart because she's a scientist.
They agree that they can still work together but Booth needs time to move on. A case pops up at Brennan's old high school, which coincidentally is having a reunion for Brennan's class at that time.
Booth goes undercover as Brennan's husband, Bobby. At the dance, a slow song comes on and Brennan wants to dance. Booth is afraid some misunderstandings might surface but accepts anyway.
Brennan confides that the reunion is like the prom she never had. The Predator in the Pool Booth and Brennan are talking about their dates for the day: As they compare their dates to each other, Booth tells Bones that she is the standard he has for women, suggesting that he still has feelings for her despite insisting that he moved on. The Rocker in the Rinse Cycle Booth is getting into the rock n' roll moment, loosening up and wearing his tie a gift from Catherine around his head.
Having convinced Brennan to join him and sing "Hot Blooded," despite the disastrous consequences last time they listened to it he got blown up , Booth and Brennan get up on stage. She plays electric guitar to Booth's vocals. The Beginning in the End As Brennan is saying goodbye to the team at the airport before she leaves for Indonesia, she sees Booth, who hasn't left for Afghanistan yet, walking towards her in the distance.
He tells her that he had to sneak off the military base in order to go to the airport to say goodbye to her. They exchange emotional goodbyes and go their respective ways.