When Damon first finds out about them, he assumes that Stefan is only with Bonnie to hurt Elena. Fucking your exes' best friend is a great to piss them off even if they longer have feelings for you. And the plan seems to work because Elena feels betrayed by both her ex and best friend. As result he decides to convince Stefan to tell him to break it off.
"If you need fuck buddy find someone who isn't connected to Elena" he says when goes to see Stefan.
Of course Stefan doesn't listen in fact his response is to tell him to get the hell out of his house. Part of him proud that Stefan doesn't seem to give a fuck, but the part of him that is in love with Elena and wants her to be happy is pissed. He knows at this point there is no talking to Stefan so he decides to go to the witch.
He corners her one night when he knows Stefan won't be with her (which was fairly difficult since they are always together at this point). It also happens that this is the one time a year that witches powers are ineffective and he uses the opportunity to scare her, knowing she can't fight back. He doesn't want to kill her, mostly because he knows Elena would be upset if he did and her spells might come in handy, but he does hope that her fear will help him in the long run.
Bonnie attempts to leave, but he blocks her way and begins to lay in to her. Damon tells her that Stefan is only doing to this to get back at Elena and asks her if she really wants to be Stefan's revenge fuck. He asks her how she could betray Elena that way and wonders how she can still be so self-righteous after that. She says nothing and instead turns to walk away. The fact that she is ignoring him pisses him off and to stop her from leaving, he grips her wrist a little too tightly and he can hear the bones break. He lets her go and she runs off holding the now broken wrist and just knows that her next stop will be to tell Stefan what happened.
He sighs because he didn't mean to take things that far and he knows once Elena finds out he'll have a lot of sucking up to do. Sill he assumes that it will be enough for Stefan to break things off with Bonnie because he will have realized that having a revenge relationship with the witch isn't worth it. He's not worried about the wrist because he figures the fallout will be similar to the fallout of when he bit Bonnie and Stefan had to give her blood to save her.
It doesn't occur to him that things have changed a lot since then and that Stefan really is serious about Bonnie until Stefan has one hand wrapped around his throat while the other hand presses a stake against his chest. There is a murder in his eyes and despite their past sordid history; this is the first time he is actually worried that Stefan might kill him.
"I'm going to say this one time." Stefan begins with a disturbingly calm voice. "Stay the hell away from Bonnie." He squeezes Damon's neck and continues. "You should be glad Bonnie cares so much about Elena because you'd be dead right now if she didn't. If you ever touch one hair on her head again regardless of how it might hurt Elena, I won't hesitate to kill you."
Normally Damon would do or say something arrogant or snarky, but this time he wisely stays silent. Stefan glares emotionlessly at Damon and says, "Are we clear?"
Damon tries to answer, but Stefan's grip on his neck is so tight that he is unable to. The look in Damon's eyes appear to be enough to convince Stefan that he will stay away from Bonnie and he slowly removes his hand from around Damon's throat. He also lowers the stake and before Damon can even blink, Stefan's gone.
The next time he sees them is a week later when goes to the Mystic Grill so he can pick up a few things for him and Elena. She has finally forgiven him for the situation with Bonnie and now they are having a sort of date night. When he walks in he notices Bonnie and Stefan sitting together. He sees Stefan carefully holding Bonnie's broken wrist. The cast she wearing is black and Stefan stares at it intensely for a few seconds before placing a soft kiss there. In response Bonnie uses her unbroken hand and caresses his cheek lovingly. They smile at each other and Stefan leans into to kiss her on the lips. They pull away after a few moments and go back to eating their meal.
Damon continues to watch them until his order is ready and he promptly leaves before either of them notices him.