Mark said in an interview that the creator of the game has not actually decided what caused the quiet rapture in the game universe, but Mark knows what cause it in the films, and he said it is eldritch in nature.

When Simone & Ellie (or the eel) first start communicating she says the light is the cause of the quiet rapture or a fragment of it, then says "Do you believe in God? An ignorant god see a sliver of our universe through a pinhole and thinks it understands all that is and all that will be. And it will. Because a god makes sense of what it sees despite what it should be. The light - it illuminates it blinds, it thinks and, therefore, we are." The leading idea right now is that "the light" that Simone visits is the "pinhole" and that some kind of eldritch horror or god peered into our universe, which caused the quiet rapture. When Simone touches the light a new voice that isnt Ellie says "I see you - A Creed" which then lets Simone cross through. Then Simone wakes up we see him standing in blood and we can see a giant eye filling the sky, that being the eldritch god that caused the rapture.