There's no way Snake can know what's going through Joker's head, but he can see the signs of discomfort on his face. Can piece together what their cause could be. Joker doesn't want him here, he's sure of it.

"'It's ok, you can stick around if you like. What did you want to talk about?' says Emily." Even Emily's voice is a little quiet, and Snake doesn't quite make eye contact with Joker as he speaks for the little snake. It's painful to.