First, I love the retro style of the art and music--really takes me back to the good ol' days of DOS gaming! I enjoy your writing style and like the idea of parallel stories, though I didn't feel like my choices had much impact.
The only other critique I would offer is to maybe differentiate which character is speaking graphically (e.g., dim or shrink the other character, or make the speaking character bigger).
Great work, as always!