In The Return, Bonnie met Katherine for the first time while at the wake for the late Mayor Richard Lockwood at the Lockwood Mansion. Katherine, who had been impersonating Elena Gilbert since she returned to Mystic Falls momentarily fools Bonnie, but once Bonnie touched Katherine and sensed that she was a vampire, she called Elena to confirm her suspicion that it was, in fact, Katherine. Realizing that her cover had been blown, Katherine attacked Bonnie, at one point lulling her into a false sense of security by pretending to be incapacitated by Bonnie's pain infliction spell. She then slammed Bonnie against the wall and prepared to bite and feed on Bonnie, only to be outsmarted when Bonnie used telekinesis to throw the doors open, forcing Katherine to stop under the fear of being exposed as a vampire by members of the Founder's Council.
Katherine successfully pretended to be Elena under Bonnie's nose in order to steal Elena's necklace, which, unbeknownst to the Mystic Falls Gang, was actually Esther Mikaelson's talisman. Since she was still on the run from Niklaus Mikaelson, she wanted to use the talisman as leverage for her freedom.
Katherine played a pivotal role in Bonnie's plan to defeat Silas in She's Come Undone, The Walking Dead and Graduation by teaming up with Bonnie and providing Bonnie Silas' Tombstone, which she had stolen from The Island, and which Bonnie needed to channel the power of her ancestorQetsiyah's calcified blood within the stone in order to drop the Veil between the living world and the Other Side. In exchange for providing the tombstone, Bonnie promised that when she summonned Qetsiyah's spirit to learn how to take down Silas, she would also ask her for the spell that made Silas immortal so Katherine could be invulnerable to any weapon, a prospect that was very enticing to the doppelgänger, whose plan to barter the cure to immortality for her freedom from Klaus backfired and who was worried about his potential retaliation.
While Bonnie and Katherine were preparing to lower the Veil to the Other Side, Bonnie magically linked herself to Katherine to ensure that she wouldn't be found by Silas and inadvertently expose Bonnie's plan to his psychic powers. This ended up working against Bonnie, however, when Elena, furious at Katherine for indirectly causing her brother Jeremy's death, caught Katherine off-guard and attacked her down in the tunnels, and every injury Katherine sustained was experienced by Bonnie as well. Fortunately for Bonnie, Stefan healed her with her blood and saved Katherine before she could be killed by Elena. In Graduation, when it became clear that Qetsiyah would not be showing up to give Bonnie the spell, Katherine became vengeful and decided to take out her frustrations on Elena, whom she believed had the life she deserved. In return, Bonnie aggressively threatened to use her Expression magic to "squash Katherine's skull like a melon," but Katherine vamp-sped away before Bonnie could harm her.
In Gone Girl, Katherine confessed to Bonnie the payback she got against Elena while a Passenger in her body by injecting her with Wes Maxfield's Ripper serum that had been mixed with toxic werewolf venom. She then informed Bonnie that she was now ready to move on to the Other Side, as her daughter Nadia Petrova was the only person who ever truly loved her and there was no longer any reason for her to keep living. However, when Katherine touches Bonnie's shoulders to pass through her as the Anchor to the supernatural purgatory, nothing happened. Katherine began to panic and asked Bonnie why she couldn't pass through her, Bonnie became alarmed and admitted that it wasn't up to her to decide. When Katherine asked who did decide, a huge opening resembling a black hole opened up in the church where they were talking and began pulling in everything around it, along with Katherine. Bonnie informed her that she could no longer help her, and despite Katherine's desperate attempts to stay on this plane, she was eventually sucked into oblivion.
The relationship between Bonnie and Katherine can be considered very different to the relationship between Bonnie's ancestor, Emily Bennett and Katherine. Emily served as a "handmaiden" to Katherine, and provided Katherine with magical assistance as needed. Katherine and Bonnie had an immediate dislike for each other and that has never changed, not even when Bonnie goes to Katherine for help with her plan to defeat Silas.
Fans find this team-up to be interesting.
Bonnie is the last person Katherine saw and spoke to in her final moments before she was dragged off into an unknown dark dimension in front of her.