The relationship between them is referred to as "Klonnie" or "Baus" by fans.
Throughout The Vampire Diaries Series
Klaus and Bonnie first met during season 2 in the episode The Last Dance, Klaus had taken over Alaric's body and had been portraying him, and Bonnie and the others were unaware they were dealing with Klaus. The gang knows that Klaus is lurking somewhere, and they are prepared to take him down, using Bonnie, who has the power of 100 witches behind her. Yet Bonnie has not mentioned that killing Klaus would kill her as well. Klaus, while posing as Alaric discovers this, and mentions it to his sidekick, Maddox, who is a warlock. Maddox informs him that it would kill any witch to use that much power, and all Klaus would need is a little provoking to do the trick. Klaus realizes he needs to get rid of Bonnie before he can get his hands on Elena, and he poses as Alaric at the Mystic Falls High School dance. Klaus corners Elena and Bonnie, and Bonnie does her best to take him down, using all of her powers. Bonnie falls to the floor dead. It is later revealed that Damon and Bonnie had secretly collaborated and decided to put a protective spell on Bonnie, so that it would appear as if she was dead. This led Klaus to believe that he had taken down Bonnie, and that she would no longer be in the way, making her the gangs secret weapon.
In the episode The Sun Also Rises, the gang is preparing to confront Klaus and the ritual. When they arrive, Klaus has already started his transition into a hybrid. Bonnie appears and throws him across the ground. Bonnie continues to cast the spell and as Klaus is weakened, Elijah approaches him. He starts to kill him, but Klaus croaks that he did not bury the family at sea - the bodies are safe. He promises to take Elijah to them if he saves him. Bonnie threatens to kill them both if Elijah doesn't slay Klaus, adding that she doesn't care if she dies. However, Elijah apologizes and dashes away with Klaus before Bonnie could stop them.
As I Lay Dying resumes with Damon suffering from a fatal werewolf bite from Tyler. Stefan asks Bonnie to summon the witches to inquire about a cure for Damon. Bonnie’s ancestor, Emily Bennett possesses her body and Stefan asks how to heal a werewolf bite. Emily refuses to give him an answer, explaining that there is a natural balance to everything and maybe Damon deserves to die. She does hint that there is a cure, though. Suddenly, Bonnie screams and clutches her head. She explains that the witches don't want her there as she is abusing their power. However, she reveals that she heard them saying that Klaus holds the key to cure a werewolf bite.
Meanwhile, a hallucinating Damon is wandering aimlessly through downtown Mystic Falls. Jeremy finds him and helps him into the Mystic Grill. Inside, Jeremy is making a call to let someone know he has found Damon. Liz arrives and shoots at Damon, but he rushes off quickly and the bullet hits Jeremy. Liz is horrified and, at that moment, Caroline and Bonnie arrive. Bonnie points out that Jeremy's ring won't work because he was hurt by a human, not a supernatural creature. Caroline feeds Jeremy her blood - much to her mother's shock - but it doesn't work. Bonnie realizes that she knows what to do and takes him away with Alaric, who has just arrived. Alaric and Bonnie take Jeremy to the site where the witches were sacrificed, and Bonnie tries to use the power of the old witches to revive Jeremy. She casts a spell but begins to worry as the other witches are angry at her for returning and don't want to help. The witches tell her there will be consequences.
Bonnie continues to cast the spell but her nose begins to bleed and she sobs. She calls to Emily, begging her to help as she loves Jeremy. However, the candles go out. Bonnie sobs as she believes Jeremy is dead for good, but then he wakes up. Bonnie hugs him and thanks Emily for helping. Later that night, Bonnie speaks to Jeremy on webcam and he reports that he feels strange, but Bonnie points out that he has just been brought back from the dead and it's bound to feel strange. It is revealed that the consequences the witches mentioned were referring to clairvoyance.
Seasons 3 picks up mid-summer and Klaus and Stefan have been traveling around the eastern seaboard searching for werewolves to turn into hybrids. Of the few they find, Klaus was not able to successfully turn them, and has become very frustrated. Klaus turns to a witch that both he and Stefan were acquainted with during their time in Chicago, Gloria.
In the episode Disturbing Behavior, Klaus and Stefan visit Gloria in Chicago, where she tells Klaus he must have done something wrong in the hybrid ritual. She also says that she can only help him if he can bring her Rebekah’s necklace, which happens to be Elena’s vervain necklace. Upon undaggering Klaus’ sister Rebekah, she cannot find the necklace. Klaus and Rebekah have Gloria, the high voodoo priestess, do a locator spell for the necklace. At that moment, back in Mystic Falls, Elena is with Bonnie and Caroline when suddenly her vervain necklace burns her chest. Gloria comes out of her trance, and has found the necklace, and includes that she saw a girl with her friends. Furious, Rebekah spats that she will be a dead girl with dead friends if she doesn't get the necklace back. At the founder's party, Bonnie brings her Grimoire to Elena and Caroline so they can find out why the necklace burned Elena. As Bonnie is researching, the necklace begins to levitate on its own. Later that day, Bonnie is searching through her grimoire trying to determine what’s happening with the necklace. Jeremy asks Bonnie if she could ask the witches for help. Bonnie replies that the witches cut her off after she used that spell to revive Jeremy, making her a less powerful witch. Meanwhile back in Chicago, Rebekah has a hunch that Stefan is hiding something, and reports this to Klaus, who breaks Stefan’s neck. In The Reckoning, upon Klaus arrival in Mystic Falls, he discovers Elena is alive, and assumes this is why he cannot successfully turn hybrids. While Elena and her friends are setting up for senior prank day at the high school, Klaus takes Elena and werewolf Tyler hostage and proceeds to feed him his blood, then snaps his neck. Klaus tasks Bonnie with finding the reason why he cannot make hybrids. Knowing there is only limited time before Tyler will really die, Bonnie races off with Matt to find Jeremy whom she believes can help her make contact with an elder witch in the afterlife who might have some answers. Here, Rebekah finds that Elena has been in possession of her necklace. Elena explains that Katherine has stolen it from her.
Meanwhile, Bonnie and Matt search for Jeremy but can’t find him. Damon and Katherine have taken him and are using him to communicate with his dead girlfriend, Anna, who may have information on how to kill Klaus. She tells them about Mikael, a vampire that hunts vampires, who has been hunting Klaus and Rebekah. They discover that Mikael has been entombed for 15–20 years, but then Damon gets frantic texts from Bonnie about what’s been taking place and he dashes off to the rescue. Meanwhile, Bonnie and Matt are still uncertain about Jeremy’s whereabouts, so Matt decides to take one for the team by drowning himself in hopes to be able to communicate with the other side. His plan works, and after Bonnie does CPR he is able to give info directly from his dead sister Vicki to Klaus that the transformations aren’t working because Elena isn’t dead.Klaus has a hunch that the original witch is lying, and does the opposite of what she says. He feeds some of Elena’s blood to Tyler, successfully turning him into a hybrid like Klaus. Klaus decides to spare Elena, keeping her around as his personal blood bank to continue creating hybrids. Damon arrives just in time to inform Klaus the he has located Mikael and he is on his way to Mystic Falls to kill Klaus.
In the episode Ghost World, the ghosts of Mystic Falls are back to haunt them. And not the smoky translucent kind either- the solid, ‘I can punch you in the face and leave a bruise’ kind. Elena discovers Jeremy kissing his dead ex-girlfriend Anna, and Mason Lockwood reveals to Damon a mysterious cave that may lead them to a method in killing Klaus. Bonnie cast a spell to get rid of the ghosts for good, by destroying Elena’s necklace, and at the very last scene, we see the necklace burst into flames, and then reappear unscathed, with a voice in the background whispering “Kill Klaus.”
In the episode Homecoming, Damon enters in a dangerous partnership with Mikael to kill Klaus on the night of the high school homecoming. Meanwhile, the newly single Bonnie and Elena are without dates to the dance. Later that night, a water valve bursts leaving the high school gym flooded, and the party is moved to the Lockwood mansion. Caroline arrives along with Bonnie. Caroline is confused how Tyler has thrown a better party than her, and also to see that Matt’s date is Elena. On the back lawn of the mansion, Klaus and Stefan are talking. Stefan tells Klaus he will bring his father to him if he will release him from his compulsion. Klaus agrees to do so. Later, we see Damon entering the Lockwood mansion with the white oak tree dagger, where he is confronted by Tyler. They begin to struggle and suddenly both sink to the floor in pain from a witch inflicted aneurysm. Bonnie appears behind them and she releases Damon from her hold, and continues to hold Tyler in his place. Meanwhile, Mikael has sent one of Klaus’ hybrids to inform him of his arrival. Klaus is angered, but goes to the front door to meet Mikael. Mikael has compelled the hybrid Mindy to bring Elena to him. Mikael cannot enter the mansion, and Klaus stands just inside the doorway for safety. Mikael provokes Klaus, telling him that he will kill Elena. Klaus calls his bluff and Mikael stabs her in the side, and she falls to the ground. Klaus stands there in shock, when suddenly Damon attacks him from behind and stabs him with the white oak tree dagger, but misses his heart. Stefan, knowing that Klaus has compelled his hybrids to kill anyone who harms Klaus, yanks Damon away from Klaus and pins him down. Elena rises from where she had collapsed, revealing herself to be Katherine instead, and throws wolfsbane grenades at Klaus’ hybrids. Klaus comes to, realizing that the white oak dagger is lying beside him, and exits the mansion, and stabs Mikael in the heart. Stefan releases Damon from his grip, and awaits Klaus to relieve him of his compulsion. When he does, Stefan looks around only to realize that Damon has gone. Later, Katherine unveils to Stefan where Klaus has been hiding his family, which are all daggered and stowed away in coffins.
The New Deal begins with Bonnie’s dream, where she is walking towards the old witch house. When she enters the house, the voices of the hundred dead witches lead her towards four coffins in the basement of the house. She then opens the fourth coffin only to find Klaus' body. She is shocked, but then notices that he has Elena’s necklace in his hands. She is startled by something behind her, and then she awakens. Later in the episode, Bonnie decides to visit the witch house in hopes of finding some meaning behind her dream. Bonnie enters the basement, where the coffins were located in her dream, only there are no coffins, but a voice comes from behind her, and she turns to see Stefan. He explains that he needs her help to keep the coffins hidden from Klaus. Stefan reveals the coffins to Bonnie, and Bonnie approaches the coffin where she had discovered Klaus in her dream, but it will not open, and they quickly conclude that it is sealed with a spell. Also, they are unsure of the inhabitant of the fourth coffin, but believe whatever is inside can help them kill Klaus. Bonnie along with help from the dead witches have spelled all 4 coffins so they are not visible.
In The Ties That Bind, we are again introduced with one of Bonnie's dreams. She is locked in a coffin and is fiercely beating on it, begging for help. Suddenly, the coffin opens, and she sees a familiar woman. After awakening, Bonnie racks her brain to find who the mystery woman is. She later reveals to Stefan and Elena that it is her mother, Abby, who left her and her father when she was only three. She believes that the dream is a message, and that her mother Abby can help her open the coffin. They discover Abby's whereabouts, and Bonnie and Elena are in route to visit her. However, one of Klaus' hybrids has already beat them to it, and has threatened Bonnie's mother. Shortly after, Bonnie and Elena arrive. Bonnie asks why her mother left her, and she replies that Mikael had come to Mystic Falls in the early nineties looking for the Doppelgänger. At the time, Elena's adopted mother, Miranda, was her best friend, and she begged her to help keep Elena safe. Abby ran Mikael out of Mystic Falls, eventually entombing Mikael in Charlotte, but she never returned to Mystic Falls. Abby no longer has any powers, and she feels that the reason is because she abandoned Bonnie, and it was the witches way of punishing her. Yet, she doesn't want any powers, and uses herbs and minerals from the earth when needed. Bonnie explains to her the situation with the coffins, and her reoccurring nightmares. But Bonnie does not believe that her mother can help her conquer Klaus with only herbs and minerals. Meanwhile, Stefan becomes concerned when he cannot reach anyone, and arrives at Abby's. But one of Klaus' hybrids has compelled Jamie, Abby's adopted son, to kill anyone who got in the way of kidnapping Bonnie. Jamie shoots Stefan with wooden bullets, which lodge very close to his heart, and ties Elena to a support beam in the barn.
Upon hearing gun shots, Bonnie springs up to her feet, but Abby quickly neutralizes her by covering her mouth with a fumigated rag. Abby drags an unconscious Bonnie to the car and takes off, while Elena, Stefan and Jamie watch. Elena and Stefan learn that Jamie has been compelled to kill anyone who interferes, and if Bonnie does not reveal the location of Klaus' coffins, Jamie is compelled to kill himself. Elena finds a loophole in Jamie's compulsion, and she knocks Jamie unconscious. Abby drives Bonnie to a secluded area on the side of the road, where she meets up with one of Klaus' hybrids. Abby begs Bonnie to tell him where the coffins are, and includes that if she doesn't, Jamie will die. Bonnie refuses, but Abby pleads with her, and texts her on to warn her friends. Bonnie complies, and warns Damon. Damon cannot remove all of the coffins before Klaus arrives, but he does manage to get the mystery coffin out. Later, Bonnie feels betrayed by her mother and asks why Abby was ready to do anything for Jamie, but had abandoned her. Abby says she would do anything for both of them, and reveals to Bonnie that when she abandoned her, that her powers drifted away the longer she was away from Bonnie. Abby believes that if she can reconnect with Bonnie, that she will regain her powers. Bonnie replies that she thought she didn't want her powers back. Abby says she doesn't, but will do it for Bonnie, if that's what Bonnie wants.
In Bringing Out the Dead, Bonnie and Abby perform a spell to release Esther from the coffin, and Esther starts her plan to kill the originals in motion. In All My Children, Bonnie lets Esther channel her power to help her kill Klaus and the rest of the originals by linking all the originals together using magic from the Bennett family, but their plan is stopped when Abby is killed and starts transitioning into a vampire. In The Murder of One, Bonnie helps Klaus unlink all the Originals after Klaus says he can help her find her mother if she helps her, while also threatening Jeremy's life if she doesn't, to which she reluctantly agrees. In Do Not Go Gentle, Bonnie works on a spell to help everyone escape from school after they are trapped their by Esther. Klaus than threatens to murder Jamie when he doesn't think she's working fast enough. However Stefan stops him, telling him that Bonnie doesn't care about them and that she won't help if Klaus hurts anyone she cares about. Klaus, Damon and Bonnie also work together on finding Esther. In Before Sunset, Bonnie works with Jeremy, Damon, Stefan and Klaus to defeat Alaric. She gives the vampire's her blood so that when they made a physical connection with Alaric she would be able to stop his heart. She uses Jeremy for this spell. Unfortunately, they failed to make a connection with Alaric but the Salvatore brothers made a connection with Klaus, resulting in Bonnie stopping his heart instead and almost killing Jeremy with her magic.
In the last episode, The Departed, Klaus is secured in a coffin while Bonnie and Damon visit him. She realizes that Klaus may have created the blood line of her friend's and family, resulting in them dying if he does. Because of this she put's Klaus in Tyler's body before Alaric can get to him and kill him. Thus far no-one knows about Klaus being in Tyler's body but Bonnie and Klaus himself. Everyone believes Klaus to be dead. At the end of the episode Klaus tells her that he's very impressed with her magic and her ability to put him in Tyler's body. He comments that he didn't believe she had it in her to do that. He also says that the spirits will be angry with her for keeping him alive. She replies by saying that the spirits didn't control her anymore, and neither does anyone else, including him.
In Growing Pains, Klaus threatens Bonnie to put him back in to his own body. Because his body didn't quite burn to ash, he threatened to rip Tyler's heart out if she didn't do as he told her. Bonnie was successful, but she and her grams suffered the consequences since she had to go deep into dark magic to save Klaus.
In A View To A Kill, Bonnie faces of against Klaus and traps him in Elena and Jeremy's living room when he tries to kill them after they killed his brother Kol. When he yells Witch, you can't do this to me! she replies by saying You have no idea what I can do now, proving that she's not going to let anyone including him-use her any more. As she leaves he scream's that he will hunt them all to their ends.
Bonnie tried to kill Klaus twice after she gained the magical strength from one hundred dead witches, in The Last Dance and in The Sun Also Rises. It is unknown if she could have actually killed him since her second attempt was disrupted by Elijah.
Bonnie's energy helped Esther link Klaus and his siblings, and she herself was the one who unlinked them as well.