His face reads 'guilty' because he knew he couldn't get away with brushing questions like that off. How was he going to explain it? That he went crazy and Matt ended up in Africa and met a man who painted Matt and the blond named Daphne with a baby and he believed it was his destiny?
He sighs some and looks at Molly for a moment. He forces a smile. "Matt and I no longer share an apartment." That was a good place to start. "I live in Queens now. Matt and his new girlfriend named Daphne live in the apartment we used to stay in. I'd gone away for a little while, and Matt ended up packing up my items, putting them away and moving Daphne in. She's a nice young woman, I'm sure you'll like her. She is special, like you. She can move incredibly fast."
He didn't really have an answer otherwise; would they be together? He didn't want Molly to feel like some sort of child of divorce, at Matt and Daphne's when it was convenient for them and while Mohinder was working. He hadn't exactly thought it all through; he even considered that Matt might be cross with him for going to get Molly in the first place.