It was a fair question, but not one devoid of ulterior motives. Bones didn't want her to go, and therefore his reason for asking was selfish. If she said she would stay, he could find comfort in her willingness to be there. If she said she would go, he would have to convince her to stay. For some reason, her wanting to leave would feel like losing her all over again, and Bones couldn't have that. He wouldn't fault her for wanting to go, of course. His own home was crowded and if she was offering up her family's home he could imagine she would want to be there, but that didn't change how he felt. These feelings were new and he hadn't fully come to terms with them yet, so he was just speaking and acting on instinct.
"I don't want you to go," he told her bluntly, leaning forward and glancing up at her. Part of him wished he hadn't left England all those years ago. Or maybe that he'd come back, even though Amelia urged him to stay in France. What would be different between them had he stayed? He wasn't sure and he couldn't look back now. "I'm rather fond of your company too."
For once, Bones was feeling unsure of himself. He didn't know where this conversation was going or where it came from or why he was feeling the way that he was. The only thing he really knew was that he wanted Mary to stay. Not seeing her every day felt strange and wrong somehow. Like he needed to make up for lost time, but what did that even entail? With their night together burned in the back of his mind, he didn't really know what to say or if he could fully articulate why he wanted her to stay. He just knew that he did.