This is a bug. I had the same thing happen, also on Dark Urge. Raphael talks about Ketheric and the tadpole while mol just stands there? I ended up going several save files back and when i reached that point again, it was how it should be- Raphael and Mol playing chess, talking about Mol giving her soul to Raphael.
I have no idea what makes that particular scene bug out, but it is a bug. You might need to go back in your saves to get it to fix itself. I'm pretty sure the game is treating Mol as if she were dead, so the dialogue Raphael has is what he'd say if Mol never made it to Act 2.
I tried to load an early save, but the situation does not change. I'll try to download even earlier saves.
