I have the plot, almost intricately so. I have the 15+ characters. I find myself looking for the why. Why am I writing this? Why would someone care? And perhaps, how will this be different than what’s gone before? And finally, are any of these questions I should be bothering with?
My instinct is to answer the last of those questions in the affirmative. Not that you can’t write a valid work without worrying about those questions. But I’m not sure I, personally, am the kind of person to do that.
I feel really positive about what I have so far, but I feel I need to throw a monumental monkey wrench in there, and my conscious mind still has no idea what that is. “What if the villain is really the hero?” “What if the main character turns out be an artificial intelligence, and we learn this near the end of the story?” That sort of thing.
When I first started wondering about these questions, I took a look at the protagonist. But he revealed nothing. I know who he is, and he seems to have depth. But he doesn’t seem to demand any more story.
Back to staring out the window.
Words are messy, but they’re the only ones we’ve got.
Corbett Buchly 
I love an element of the fantastic in any story…but subtle. Think Steve Martin having a relationship with a traffic sign in LA Story (and the traffic sign really wanting to be a set of bagpipes).
My favorite school of writing is probably Absurdism. The film Being John Malkovich is a great modern example….So, I’m agreeing with you. I’m not entirely sure the story I’m writing will admit that sort of thing, but you’ve inspired me and I plan to explore it. More on this later.
Recently finished Downtown Owl by Chuck Klosterman. It’s not really a story so much as an exercise in character development, and then an abrupt ending. One could consider the ending a monkey wrench of epic proportion. For me, that sort of thing forces a deep love or extreme hatred for the book (I loved it). It leaves no middle ground.
The reason, i mention this is because you wrote “I took a look at the protagonist. But he revealed nothing. I know who he is, and he seems to have depth. But he doesn’t seem to demand any more story.” Similar, it feels like Klosterman painted himself into the corner with a fantastic character that left Klosterman with no where to go but the nuclear option.
I am, in fact, at this moment looking at a whole toolkit of monkey wrenches.