(Takes place in season 1, episode 14)
Bonnie stayed at Elena's house for the rest of the night—her father was still at work and unable to leave—and Bonnie needed to be comforted for a while. Because Bonnie's Grams had been more influential to her than her father had ever been, she cried for what seemed like hours, with Elena constantly by her side—comforting her when it was possible.
Then, when the crying was over, the two watched a few movies to distract themselves from Tituba (Sheila) Bennett's death. But the two girls eventually became tired and they decided to go up to Elena's bedroom to sleep, and did so as soon as they hit Elena's big, fluffy comforter.
A while later, when the two girls were deeply asleep, Elena's window slowly creaked open and a crow flew in, landing quietly on the headboard above Bonnie's head. Less than a second later, Damon himself appeared, walking silently through that same window. He looked at Elena's sleeping form for a minute, appearing to have an inner conflict, before he approached Bonnie. He let his hand brush a stray hair away from her face before quietly speaking.
"I am sorry that your grandmother died, and I am sorry that I had more than some fault in her death. Sheila was a very powerful witch, a very respected one at that, and this town will be all the poorer without her." Damon let his fingers linger on Bonnie's cheek, feeling her soft skin under his hand. But then he saw her brow crease and he quickly ghosted from the room.
When Bonnie opened her eyes moments later, she was alone, except for Elena—who was still sleeping. Though she couldn't see anything, Bonnie still felt as if someone had just been in the room, brushing their slightly callused fingers over her cheek. And randomly, so Bonnie thought, she felt less enmity towards Damon, though she couldn't manage to put a finger on why. Touching her face again, Bonnie reassured herself that no one else was there, and fell back asleep.
Meanwhile, outside, standing on a tree branch, Damon Salvatore still watched. "Sleep well little witch," he whispered. "This town will be needing you soon."