While Booth and Brennan maintain a professional relationship and friendship, there is also the beginning of a romantic tension within their relationship. Both clairified their relationship as professional only, though people often assumed they did have a sexual relationship. The other "squints" think there is something between them by hearing their strange conversation. Brennan stated she didn't understand why Booth is "needlessy protective sometimes" to Agent Perrota in The Princess and the Pear and asked why people always think they have a romantic relationship when they barely touch each other, which she asked twice in The Passenger in the Oven.
In season 1, Booth arrested Brennan for shooting a murderer who, despite trying to set her on fire, was unarmed at the time. Even though she was not convicted, she was still charged with a felony, which meant that her original application for a concealed weapon was denied. In the second season, she was allowed a permit.Booth is shown to be jealous of Temperance's romantic relationships in Two Bodies in the Lab and The Woman in Limbo. He is known to be fiercely protective of both Brennan and his partnership with her. When he was asked by his potential love interest Camille Saroyan, what he would do if she fired Bones, he instantly replied "I'm with Bones, Cam. All the way. Don't doubt it for a second." in The Boy in the Shroud. When her life was in danger, he went out of his way to be with her and protect her himself. In Two Bodies in the Lab, when Bones was kidnapped, Booth, despite having recently barely survived a deadly blast intended for Bones, took part in the rescue mission to find her even though he was horribly hurt. Perhaps Booth's most famous example to date was when he tracked a gang leader who put a hit out on Bones and threatened the man himself, sticking a gun in the criminal's mouth and saying "If anything happens to her, I will find you and I will kill you. I won't think twice," in The Woman in the Garden.
Booth and Brennan tend to spend more and more time together outside work as the series goes on, having lunch then dinner, preparing their quotes for trial together. He went with her to China and to London. In the fourth season, Brennan often goes to Booth's house. This habit actually led at one point to Brennan seeing Booth naked; she broke into his house using a hidden key and walked into his bathroom, without knocking, while Booth was in the tub reading a comic book. While talking to him she unwittingly insulted him as she usually does making him stand up in anger exposing himself to her, despite Brennan's usual cold, logical almost emotionless approach to sexuality she appeared to be slightly flustered in this instance.
Their close friendship often leads to their contrasting personalities being pointed out. Booth is a people person who relies on inferences and bluffs to continue an investigation where as Dr. Brennan only uses facts to continue a case, so much so that she will state when someone hypothesizes in the lab. In the episode, "The Parts in the Sum of the Whole", Bones said that she did not want to be in a relationship because she did not know how to change herself and that she did not have the open heart that Booth did. She accepted Booth's subsequent conclusion that he needed to move on, although he agreed that they could still work together.
Although Booth went on to have a brief relationship with Dr. Catherine Bryar, a marine biologist they met on a case, his subsequent comment that he considers Brennan his "standard" for other women suggests that he still has feelings for her, with Brennan herself showing some emotional conflict over the decision, to the point that the two take a year apart to pursue other projects with their lives (although both agree to meet up again the following year).
When they reunited after seven months apart to help Cam with a difficult case, Booth was now involved with Hannah Burley, a journalist he met while stationed in Iraq, with Hannah later moving to DC to be with him while Brennan was forced to re-acknowledge her feelings for Booth. However, after Hannah left when Booth's awkward attempt to propose revealed that she had no interest in marriage, Booth and Brennan began to re-explore their relationship, culminating in Brennan becoming pregnant when they slept together following the death of Vincent Nigel-Murray at the hands of Booth's old mentor-turned-enemy Jacob Broadsky.
- Episode 13: The Woman in the Garden
When a gang leader puts a hit out on Brennan, Booth tracks him down, puts a gun in his mouth and tells him that if anything happens to Brennan, Booth will kill him without thinking twice about it.
- Episode 15: Two Bodies in the Lab
Booth is injured in a bomb explosion meant for Brennan. Despite this, when Brennan is kidnapped and threatened by the rogue FBI agent, Booth leaves the hospital to find Brennan. Despite being severely injured, he lifts Brennan up from a hook that she was hanging on. This is the first time they hug on screen.
- Episode 19: The Man in the Morgue
When Brennan wakes up covered in blood, with no memory of the day before, Booth travels from D.C. immediately even though Brennan told him, it was not necessary. When Brennan becomes a suspect in a murder investigation, Booth hides evidence (Brennan's earring) placing her at the crime scene; staking his career on the belief that Brennan could not murder anyone.
- Episode 21: The Soldier on the Grave
Booth and Brennan share an intimate moment at the end of the episode. Brennan puts her hand on Booth's arm whilst he's telling her one of his biggest secrets and he puts his hand on hers and strokes it.
- Episode 8: The Woman in the Sand
Seeley is extremely impressed when he sees Brennan in a somewhat revealing dress he picked out for her, and slaps her butt later in the episode to convince others they are a couple while undercover as a street fighter, Tony, and his "sugar mama" Roxie.
- Episode 14: The Man in the Mansion
Agent Sullivan invites Brennan out on a date and asks Seeley for advice. When Seeley refuses, Sullivan asks "It's not like you have the hots for her." To this, Seeley doesn't deny but sputters an almost agreement.
- Episode 18: The Killer in the Concrete
Brennan, after discovering Booth's tooth at a hotel, punches the bounty hunter Veleska Miller in the face screaming "Where's Booth?!" after she tried to escape the scene of Booth's abduction. She would have continued, if not for her dad restraining her arms while she screams "Kennedy has Booth, Dad. He's got Booth!"
- Episode 8: The Knight on the Grid
While in the hospital Bones kisses Booth on the cheek to thank him for letting her brother see his daughter before he turned him in. Booth and Brennan got bombed while tailing a serial killer and Booth helped Bones out of the car.
- Episode 9: The Santa in the Slush
Max wants to spend Christmas with his family, so Brennan decides to ask Caroline Julian, though Booth says that she will want something in return. Caroline does indeed want something; she wants Brennan to kiss Booth on the lips for 5 steamboats (seconds), and under some mistletoe. The two kiss, and to the shock of Caroline (and themselves), the kiss lasts for 10, not 5, steamboats. Booth ends up with Brennan's gum in his mouth after the kiss. This is their first on screen kiss. Also, he brought a decorated Christmas tree (with the help of his son, Parker), and set it up outside the jailhouse trailer.
- Episode 12: The Baby in the Bough
A woman's car is run off the road and she is killed, but her baby miraculously survives the accident. Bones, with the help of Booth, takes care of the victim's child. Throughout the case they both form a bond over the child and by the end of the episode Bones and Booth act like the parents of the baby. Booth even saying, "Our little guy is going to be just fine", but corrects himself to, "He is going to be just fine".
- Episode 13: The Verdict in the Story
Booth and Brennan are adamant that they do not want to stop working together whilst Max's trial is pending. Booth goes from being irritated that Brennan is laughing at him, to stating it doesn't bother him when their partnership is threatened. Booth doesn't want to take the stand against Brennan and her father. He also states that he knows Brennan and that she would not be capable of the crime that her father Max is on trial for.
- Episode 14: The Wannabe in the Weeds
When Booth's stalker, Pam Nunan gets jealous of Brennan, because of the way Booth looks at her, she shoots Booth. Brennan then goes to Booth and before Pam shoots her, Brennan shoots her through her throat.
- Episode 5: The Perfect Pieces in the Purple Pond
After Booth was complaining about his back aching the entire episode, he finally let Brennan help him with it. She gets behind him, puts her arms around him, and straightens his back out, followed by some circular motion. Once she's finished, he thanks her, and exclaims how happy he is that they're partners.
- Episode 11: The Bone that Blew
Brennan's father, Max, asks Booth if he's sleeping with his daughter. Booth looks confused, telling him a clear "no." Max asks whether that it's because Booth is gay, he doesn't find Brennan attractive, or if it is because of his (Max's) criminal past. Booth answers no to all claims, even proclaiming that he thinks that "Bones is beautiful." Max then tells Booth that he's a "good man, and "[he] want[s] that for her," suggesting that he would approve of the two being in a relationship together.
- Episode 12: Double Trouble in the Panhandle
While posing as a married Canadian knife-throwing act to infiltrate a traveling circus, Sweets, who looked after his biological mother at a circus and therefore has insightful knowledge in that field, advises them that they should look like they're more interested in each other than in their fellow performers and the circus staff. They therefore figure they should rock their mobile home so that it looks like they're having sex in there - with great success, as the ringleader believes it. Later, they even argue over the tidiness in their mobile home, which also only has one double bed. Before their act, Booth compliments Brennan on her Russian knife-throwing costume.
- Episode 13: Fire in the Ice
After a hockey game that Booth played and got injured in, Brennan barges in on Booth talking to Wendell (also a player) shirtless in the men's locker room to see if he is okay. When he falls and passes out in another game, Brennan admits that she gets nervous when Booth falls and gets hurt. In the last scene, they go ice skating at an empty rink, and Brennan tells Booth he's the only FBI agent she would want to work with. Booth says that nothing is going to change between them.
- Episode 15: The Princess and the Pear
Under the influence of strong pain medication, Booth tells his substitute Agent Perotta to protect Brennan while he is gone: "If anything happens to her, you know, that silky black hair and that soft skin..." In the final scene, Brennan is fixing Booth's back when Agent Perotta comes to drop off some food for Booth and thinks she caught them in the middle of an intimate moment.
- Episode 16: The Bones that Foam
Booth and Brennan go to a stripclub to talk to a stripper that gave the murder victim a lap dance on the night of his death. The stripper gives Booth a lap dance, figuring that Brennan, who pays for it, is his girlfriend who wants to watch.
- Episode 19: The Science in the Physicist
Hodgins and Nigel-Murray do an experiment that explodes just as Booth and Brennan are nearing the room they're in. Booth immediately pushes Brennan up against a wall to protect her from the blast.
Later, when the murderer is caught and done with, Booth tells Brennan that she is the only smart person he really likes.
- Episode 20: The Cinderella in the Cardboard
Dealing with a victim that had plastic surgery on her toes, the surgeon offers to leave Booth and Brennan after they start one of their discussions so that they can continue their lovers' spat, but they assure him that they only work together. Later, they visit a bridal shop where the owner tells them that they are obviously meant for each other. Incidentally, Booth ends up setting up a hypothesis for Brennan asking her what she would do in a situation if they were going out. Brennan confides in Booth that she is jealous of Angela, Cam, Booth.. etc.. because they all want to lose themselves in another person and be in love.
- Episode 21: Mayhem on a Cross
Dr. Gordon Wyatt comes back and talks to Sweets about his book about Booth and Brennan. He compliments him on his work. "This is probably the best work I have ever read on the dynamics of opposite personality types working towards a common cause," Wyatt says but then critiques him in his statement that Booth and Brennan are opposites in personality. Sweets then asks whether Wyatt agrees they have sublimated their attraction to each other so as not to endanger their working relationship. Wyatt disagrees again, saying, "One of them is acutely aware of that attraction; struggles with it daily, as a matter of fact." Sweets asks who, but Wyatt just says that that is for him, as the writer of the book, to figure it out, which he does. In the final scene of the episode, when Booth and Brennan found out about Sweets' abusive childhood and decide to share some of their traumatic memories from when they were younger, the two have a moment in his office. The original title of Sweets' book "Opposites Attract: Yin and Yang in the Workplace" is crossed out and changed to "Bones - The Heart of the Matter."
- Episode 22: The Double Death of the Dearly Departed
Brennan promises that if Booth were to die before her she would visit his grave every once in a while and talk to him. When he asks her why she agreed, she explains that if she were to momentarily pretend that he was still alive, it would make her feel better for that time.
- Episode 25: The Critic in the Cabernet
Brennan decides she wants a child and asks Booth to be her sperm donor. He agrees, and in a session with Sweets, Brennan is asked why she chose Booth instead of an anonymous donor at the sperm bank. She answers that Booth has traits like courage, compassion and empathy that doesn't get cataloged in sperm bank files. But when Booth has a hallucination of Stewie Griffin in the interrogation room with Brennan, he tells Stewie that he doesn't want Brennan to have a baby with his sperm if he can't be involved in the baby's life. Brennan pulls Booth out of the room, and he tells her about Stewie. Brennan realizes there is something wrong with Booth - he also had hallucinations of Luc Robitaille (Fire in the Ice) and his military friend Edward Parker (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.
- Episode 26: 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. She was pregnant.
In the real world, Booth wakes up from his coma and doesn't recognize Brennan.
- Episode 1: Harbingers in the Fountain
He begins to tell Brennan that he loves her but sees a clown and isn't scared of it like he used to be, so he begins to rethink Sweets' theory. He then tells Brennan that he loves her - only in a "professional and atta girl kinda way." Brennan responds by telling him she loves him in a "atta boy kinda way."
In the end of the episode, Avalon tells Booth that her cards tell her that "this all works out eventually."
- Episode 2: 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.
- Episode 4: 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.
- Episode 5: A Night at the Bones Museum
Brennan goes on a date with Booth's boss' boss, Andrew Hacker. 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. "What goes on between us is ours," he explains to her. 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.
- Episode 6: 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.
- Episode 7: 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.
- Episode 8: 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." Booth doesn't explain, but it is evident he had complimented her to his grandfather. 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.
- Episode 10: 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." Brennan later tells her second cousin Margaret Whitesell that she finds Booth "quite pleasing to look at."
- Episode 16: 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." But they argue about the case, leading Brennan to slap Booth. 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.
- Episode 17: The Death of the Queen Bee
- Episode 18: The Predator in the Pool
Booth and Brennan are talking about their dates for the day: Booth with Dr. Catherine Bryar, a marine biologist, and Bones with Andrew Hacker, the Deputy Director of the FBI. 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.
- Episode 19: 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.
- Episode 22: 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.
- Episode 1:The Mastodon in the Room
Booth reveals that he is in a relationship with Hannah, a reporter he met in Afghanistan. Later, when Brennan and Angela are discussing this, Brennan says she is OK with it, but Angela appears unconvinced.
- Episode 2:The Couple in the Cave
Booth and Brennan are puzzled over a case involving a male and female victim whose remains were found in a cave. When they died, the man was embracing the woman. His injuries weren't as severe as his companion's, but he didn't leave her to go for help. After Booth and Bones identify the bodies, they realize that the two people — who were obviously romantically involved — were of completely different socioeconomic backgrounds. Booth, Sweets, and Bones discuss the case over lunch at a diner, and Bones says when people are opposites, it can sometimes work out. She admits that she used to imagine herself and Booth together. Of course, being Bones, she says this so matter-of-factly that Booth almost drops his spoon. Sitting awkwardly between them, Sweets asks if they want to be alone, but they don't.
- Episode 9: The Doctor in the Photo
Booth and Bones work on a case involving a woman found dead in a bad neighborhood. As Bones delves into the victim's past, she identifies herself with the victim more and more, to the point of talking to the victim through her tapes. The victim's voice tells Bones that she died with regrets, especially regarding her personal life, which prompts Bones to tell Booth that she doesn't want to live with regrets, that she made a mistake in not giving them a chance. Booth, however, rejects Bones, telling her, "I'm with someone, Bones. And Hannah? She's not a consolation prize. I love her. You know, the last thing I want to do is hurt you, but those are the facts."
- Episode 13: The Daredevil in the Mold
Booth meets Hannah in the park. Hannah is ready to have a nice dinner with her boyfriend, but Booth has other plans. He proposes, but Hannah tells him that although she loves him, she's not the marrying type. Booth ends up breaking up with her. Later Booth is at the Founding Fathers, having a drink, and another, and another. Brennan shows up, saying that Hannah called her after the proposal. Booth is reluctant to say anything about it. He feels like he's going to be alone forever, and he wants to give Brennan a choice. Stay and be his partner, or leave so that she can have a new FBI partner in the morning. Brennan decides to stay and have a drink with Booth.
- Episode 14: The Bikini in the Soup
While everybody else in the Lab is really excited about Valentine's Day, Bones and Booth (still recovering from his break-up) try to turn down the significance of Valentine's Day. After the murderer is caught, Cam makes her romantic date with Paul, Clark decides to fulfill his girlfriend's fantasy by being Cupid, and Hodgins creates a mold in Angela's name...which she loves. Booth decides to go to the shooting range, and Brennan joins him with a gun he's coveted, commemorating St. Valentine's martyrdom.
- Episode 15: The Killer in the Crosshairs
Bones is running and then Booth comes and joins her. They then race with booth taking a head start and having Booth buy them both coffee. Booth asks if Bones is still going to a lecture about the Peloponnesian war and asks to come for company. Booth doesn't like it when Bones tells him that he's like Broadsky, but then later states what he does is good and different from what Broadsky does.
- Episode 16: The Blackout in the Blizzard
Bones and Booth sit in the Vets seats inside Booth's apartment. Booth says he just "needs time" before he "gets back out there." Bones says she is becoming stronger.
- Episode 22: The Hole in the Heart
After the death of Vincent Nigel-Murray, Booth told Brennan to sleep over at his place. The next day, Brennan tells Angela that she "got into bed" with Booth. As Bones talks to Angela about the other night, it is heavily implied that they slept together. In the next episode, The Change in the Game, it is confirmed that they did, because at the end of the episode, Bones reveals that she is pregnant with Booth's baby.
- Episode 1: The Memories in the Shallow Grave
A very pregnant Brennan and Booth are a couple but are going back and forth between apartments. Booth suggests that they should have their own place, whereas Brennan wants Booth to move into her apartment. It causes a minor rift between them but is resolved when Booth admits why he wants to move into a new house. Brennan, having some time to think it over, says it's a good idea because she'd need him practically, emotionally, and sexually. At the end of the episode, they are in bed looking at houses on-line. This is also a noteworthy episode in that for the first time, both Brennan and Booth say "I love you" to each other.
- Episode 4: The Male in the Mail
Dismembered remains are discovered in several boxes at the dead letter office. Meanwhile Booth's grandpa comes to town with the news that Booth's father has passed away. Brennan is at first unable to comfort Booth but at the end of the episode she tells Booth "for the time being we are sharing our lives and that means you can't shut me out Booth" which highlights the almost marital relationship they have and that Brennan is becoming more understanding as a spouse. Later, they reminisce about the fond memories of his father.
- Episode 7: The Prisoner in the Pipe
Small parts of a body is found in a toilet in a house and leads the team to finding that somebody was killed in a prison. Brennan and Booth are arguing about where the child should be born. When Brennan goes into labor, they are turned away from an inn, and are forced to go to a barn which has Booth making connections to his religion and once their daughter is born, Brennan admits there is a mystery to life. Later, they celebrate the welcoming of Christine Angela Booth.
- Episode 9: The Don't in the Do
While investigating a blue dyed murder victim, Bones starts feeling self-conscious about her post baby body making Booth unsure about the right thing to say. In the middle of the Episode Sweets talks Booth into a lingerie store to buy things for Bones. Although Booth seems uncomfortable he does ends up buying some for Bones and they tease each other at the end of the show about her wearing it and about her feeling good in her post baby body.
- Episode 13: The Past in the Present
Caroline, Booth and Brennan are in a court room with a hacker,"Pelant",who says he isn't the same guy anymore. Booth and Brennan are at home arguing about how Brennan is the main suspect in the case of her dead friend. More evidence points to Brennan. Booth and Brennan are getting their daughter baptised, Booth tells Brennan he is going to get the car, but Brennan calls him over to her. She tells him that she loves him and that the baby is not the only reason they are together, then they kiss. Booth tells her everything will be okay and he kisses the baby's forehead. When Brennan's dad shows up in another car, she puts the baby in first then she gets in, Booth notices whats going on and runs after the car. He tells her dad to tell her that,"he is going to get his family back"and sits on the church steps crying.
- Episode 1: The Future in the Past
With Bones on the run, Booth is mad at Angela for somehow contacting Bones for the past 3 months about Booth and the Pelant Case. But when Booth shows up at the motel Bones is staying at (near a crime scene she anonymously called in to the FBI and told Angela, through their secret communication, was something to help Bones be cleared for the murder of her friend whom Pelant killed), Booth attacks Bones to the floor as she comes in the door, thinking it was someone about to attack him, but when he recognizes her they kiss on the floor. As the show goes on about clearing Bones' name Booth gets to keep his daughter (now able to say da-da) around him and kiss Bones. At the end of the episode she re-dyes her hair back to her normal color and tries apologizing to Booth about running off. He says it was the right thing to do, but Bones is weighed down with guilt from having left for the 3 months. Booth consoles her by kissing her and they get carried away, taking Booth's shirt off, and lifting Bones up onto the washer making out, when they get a horrible phone call (with Bones wanting Booth not to answer it) ending the moment. They end up at the FBI, and as the show ends, Pelant has gotten himself cleared of all charges by creating an electronic trail that shows he is not Pelant, but an Egyptian citizen, who will be immediately taken out of the U.S. by the Egyptian government.
- Episode 2: The Partners in the Divorce
With Bones back, Booth and her start butting heads starting with Bones making breakfast and turning away from Booth. They argue about putting Christine on a charosel because Bones put her on one in Connecticut and she didn't like it. Booth starts to get agitated that Bones is acting like she wishes she is out there and he starts yelling about it while Bones rationalizes how she wont yell back at him because he is mad at her. At the end of the episode Booth apologized and Bones tells him what Sweets said about her overthinking things in there relationship because she doesn't want to ruin it, the conversation ends with them kissing to make up and joking about how Booth will fart while kissing to make it less formal. Booth says that he feels like he can't make up for the three months that Bones was with on the run with Christine and that he doesn't want to lose them again.
- Episode 4: The Tiger in the Tale
Bones is making a pros and cons list for herself on if she would make a good president. While she thinks that her background with law enforcement and her knowledge of other forms of government would be beneficial, Booth argues that her being a former fugitive doesn't help her case. When Bones and Booth discover that a suspect shot and killed an endangered Siberian Tiger, Bones becomes upset, charging at the man. Booth grabs her before she can get to him. She cries into Booth's shoulder. At the end of the episode, Booth has on a bunch of campaign buttons for Bones. They laugh and have sex.
- Episode 6: The Patriot in Purgatory
After solving a case about a man who rescued people from the 9/11 bombing on the pentagon, Bones admits to Booth that for two weeks, she unraveled the mysteries tied to the remains from the buildings in the attack without shedding one tear. While at the time, she thought that made her strong, she now has Booth. He has made her realize that it could have been him she was pulling out of that building. She cries and he pulls her into him as she sobs into his shoulder.
- Episode 9: The Ghost in the Machine
At the end of this episode Booth surprises Bones with a mixed tape on an iPod (with a double earphone jack so they can listen and be close together) that starts with "their" song Hot Blooded and they dance around the kitchen with Christine. This is also an episode where Booth and Bones have a rare emotional moment, As he calls Bones Temperance and craddled her in his arms when she had a moment of crying in the lab about how the kid they were investigating was a kid and how young he was, showing how being a mother has opened her to the motherly/humane bond to children and family.
- Episode 10: The Diamond in the Rough
Booth reveals to Brennan and Sweets that, years ago, he used to be a dance teacher. Sweets tells him and Brennan to go undercover to solve the case on going, since it was all about dancers in a TV show. At the end, they finally catch the murders, but Brennan still wants to dance with Booth in front of the audience. Booth agrees even when he knows Bones isn't really good at dancing, and they end up dancing a slow, romantic vals.
- Episode 15: The Shot in the Dark
Booth and Brennan fight over a family matter which ends with Brennan misunderstanding Booth, thinking he called her a bad mother. Bones goes to the lab to spend the night there and gets shot by another member of the Jefferssonian; Booth goes to apologize but finds her bleeding out because of the shot and Brennan is taken to the hospital. Her heart stops beating for 2 minutes during surgery, she was technically death for all that time, and has an hallucination where she sees her mother. When she's awake again, she tells Booth that she thinks he could've been the reason why she "always came back", meaning she went back to life for him. At the end of the episode, they talk about Bones' hallucination and Booth tells her "it's okay to be a little crazy" and they laugh and kiss.
- Episode 24: The Secret in the Siege
Brennan returns from shopping and claims the supermarket was out of jerky, but when Booth notes they're only out of it when she does the shopping and that he knows she's lying, she laughingly admits it. Bones then admires how happy Booth's mom looks in her honeymoon picture and Booth notes that "marriage is starting to look good on you." Bones immediately protests "I'm not going to propose to you, if that's what you're thinking." But Booth says the fact that she caught the bouquet at the wedding when she's usually awful at catch proves she subconsciously wants to marry him. She denies it, but reassures him that she loves him and asks isn't that enough. He assures her it is, they banter some more then are called in on a new Pelant case. When it's revealed that all the victims are FBI agents, Bones is visibly upset and tells Booth he is not allowed to die. He promises he won't. As events worsen, she calls and tells him to meet her. He rushes to the Jeffersonian gardens where she's anxiously waiting. When he asks if she's alright, she gives him a bag of jerky and says "I wanted to give you this. I should've bought it for you before. If you like it I want you to have it. I want you to be happy...that's all I want." He again reassures her that he's going to be fine, but in typical Bones fashion she disputes this, enumerating all the terrible things that could happen to either of them. She then says, "The point is, I want to marry you. Will you marry me, Booth?" Moved beyond words, Booth finally says, "Yes, of course." They kiss, unaware they're being watched by Pelant's cameras. Brennan and Booth, respectively, share their happy news with the squints and Sweets. Sweets warns Booth that Pelant needs to feel he's the most important thing in their lives and their engagement may cause him to escalate. Booth says he's waited a long time for this and he's not going to let Pelant ruin it. Later, Booth, Bones and Christine are at a playground when Pelant indeed calls Booth to say he can't marry Bones and can't tell her or anyone the reason why he's turning her down, or else he'll be responsible for the deaths of five innocent people. He describes five random people in Booth's vicinity so he knows they're being watched, and taunts Booth that since he's read everything Sweets has ever written about him and Brennan, he knows they would never trade those people's lives for their own happiness. Booth tells Pelant he's going to kill him, but as turns and sees Bones smiling at him, he knows he's trapped and that he's going to hurt her badly. At the end of the episode, as Bones is curled up on the couch happily discoursing on the bridal magazines Angela gave her, Booth tells her they need to talk about the wedding and says, "I don't think we should do it." Confused, she asks why not. He haltingly explains that he knows it's not really what she wants, as she never wanted to marry before. She almost timidly assures him, "But I do now." He gently insists that she's actually just reacting to the Pelant situation, that it's not really a good time and, finally, that she was right earlier when she said they love each other and what they have now is enough. Eventually, her walls go back up and she agrees, claiming she's impressed he's finally come around to her way of thinking. As she rushes to leave the room, he stops her and asks if they're okay. She says, "Of course," but he knows she's covering. Once out of sight, Bones gives in to tears as she goes upstairs, while Booth sits downstairs devastated.
- Episode 4: The Sense In The Sacrifice
Bones goes to a warehouse where she knows Pelant is. When Pelant finds her she pulls a gun on him and makes him walk down stairs, he then causes an explosion and Bones is defenseless. He talks about how Booth is a sniper and too slow, which he's not slow, and then Booth pops up behind Pelant. Pelant then threatens to blow up the whole place, but Bones tells Booth to shoot him. Booth shoots Pelant before he hits the trigger button. Booth then proposes to Bones, she accepts as the Jeffersonian team watches from the lab.
- Episode 6: The Woman In White
The team gets ready for Booth and Bones' wedding when a body is found. Everyone on the team tries to keep Bones as far away from the case as possible, to keep her focused on the wedding. When the case is solved, they are getting ready to go to the rehearsal dinner when Sweets knocks on the door and tells them to turn on the news. They do, and they see that the church they were going to get married in is on fire.
Booth and Bones decide to postpone the wedding, but Angela takes the matter into her own hands and arranges a wedding outside in the spot Booth and Brennan first agreed to work as partners. They exchange vows, and they get married.
- Booth: "You know, I worked really, really hard on my vows, but you know, now that we're here -- look, hey, do you remember the last time that we were here, standing right around this spot? It was right in the beginning, before we really knew each other. I was trying to get away from you, because you were irritating me, and you chased me down and you caught up to me. I said to you, "Listen, I just have to get all my ducks in a row," right, and then you said to me--."
- Brennan: "I can be a duck."
- Booth: "Yeah. We had been chasing each other for a long time, been chasing each other through wars, and serial killers, and ghosts and snakes, and chasing you has been the smartest thing that I have ever done in my life, and being chased by you has been my greatest joy.But now, we don't have to chase each other anymore because we caught each other."
- Brennan: "When Hodgins and I were buried alive, we each wrote a message to someone we loved, in case our bodies were ever found. Hodgins wrote to Angela, and I wrote to you. *takes out letter* "Dear Agent Booth, you are a confusing man. You are irrational and impulsive, superstitious and exasperating. You believe in ghosts, and angels, and maybe even Santa Claus, and because of you, I've started to see the universe differently. How is it possible that simply looking into your fine face gives me so much joy? Why does it make me so happy that every time I try to sneak a peek at you, you're already looking at me? Like you, it makes no sense, and like you, it feels right. If I ever get out of here, I will find a time and a place to tell you that you make my life messy, and confusing, and unfocused, and irrational, and wonderful. This is that time, this is that place."
- - The Woman in White
Brennan: I'm... quite strong.
Booth: Yeah, well, you've always been strong.
Brennan: You know the difference between strength and imperviousness, right?
Booth: Well, not if you're going to get all scientific on me.
Brennan: Well, a substance that is impervious to damage doesn't need to be strong.
Brennan: When you and I met — I was an impervious substance. Now I'm a strong substance.
Booth: I think I know what you mean.
Brennan: A time could come when you aren't angry any more and I'm strong enough to risk losing the last of my imperviousness. Maybe then we could try to be together.
Booth: I am going to write down a date. A guess when that time is. I want you to do the same.
Booth: Why? Because when I was a kid if I wanted something really, really bad, I’d write it down on a piece of paper and I’d burn it. It was like a spell. It was bound that my wish would come true.