What do you think have caused this?

I don't know if they left any clues or not. To be honest, I don't think they really cared about what the cause was. I think it was just a device to set up their purpose.

And it seems to me that the writers' purpose was to explore what might happen if two lovers were the only people left on earth. How would their world views shape how they responded to the situation? How would their differing world views affect their relationship?

It's a shame this is labeled as science fiction because it doesn't really have any science fiction elements other than the strange light that preceded everyone disappearing. Calling it science fiction sets it up to fail with people who expect science fiction.

Given the growing flash Jenai sees the night before, it was some huge phenomenon. I thought of it as a weapon gone wrong. To be instant like that, I figured something that transported most everyone into another dimension.

Like the "effect" in the (better) film, "The Quiet Earth." Be sure and see that if you haven't!

Come to think of it, it might not have "gone wrong." Note how many "elites" these days want to wipe out 2/3 or more of humanity as a "cancer" or "disease" on the Earth. Of course, they don't lead the way by committing suicide... unfortunately.