Disclaimer: All of these characters belong to people who aren't me.
Author's Note: This story was written in response to a challenge at tvd_las on Livejournal. The challenge was "[character] switches sides."
When Bonnie made the decision, it had made perfect sense. After all, she and Katherine had very similar goals. Bonnie would have sided with her on killing the tomb vampires, of course, had she known it was an option. Now, the witch could keep an eye on the most dangerous vampire in town, and Katherine's main goal and Bonnie's lined up perfectly:
Get the Salvatore brothers out of Elena's life.
Bonnie should have known that Katherine meant 'by any means necessary.'
Killing Damon wouldn't be a problem for her. Maybe once it would have been, but that had been before he tried to kill her, and before Caroline had been turned by Damon's blood. She would have a bigger problem killing Stefan, since he seemed to honestly try to be good, but Bonnie could sense that Katherine wanted Stefan dead even less than she herself did, so she didn't think the problem would even come up.
But on the subject of Elena, the two couldn't differ more. Katherine would have no issue with killing Elena, but that wasn't the problem. The problem was that the vampire thirsted for her doppelganger's blood more than Bonnie could ever have imagined. In Katherine's mind, Elena had stolen away two valuable pieces of her property. Stefan and Damon were toys that sat on her shelf, unused and gathering dust, but that didn't mean anyone else was allowed to play with them. Once Bonnie figured that out, her original plan of helping Katherine to get the Salvatores out of town no longer made so much sense.
Turning on Katherine openly would mean the end of her; there was no doubt about that in Bonnie's mind. But all of her subtler attacks were just shrugged off. She didn't even notice when her meal had ingested vervain, though she didn't kill him. That was the one thing Bonnie had gotten out of their deal.
She'd thought she was so clever, working against Elena to ultimately save her. Now, all she could do was work both sides of the fence and pray that, when Katherine decided to make her move, she'd be able to warn her friends in time.