Really cool idea! Looks and sounds great, too!
That said, I cannot for the life of me get even the first chapter to work. I've put together a sequence that, to me, makes all the sense in the world -- but the game insists it's wrong. It's frustrating that there is no way to determine which of the squares is not in its right place (could the wrong element perhaps be highlighted? Or could there be a way to test an unfinished sequence before adding more elements?)
Another minor thing: it would be good to have a way of fast forwarding to the next frame in the chapter in addition to skipping the entire chapter (which is what a left click currently does).
Finally, I wonder if, for the full story, the mechanics would work without spoiling too much of the story? Or is it the point for the player to figure out what happens before they see the complete sequence? I would consider having frames containing key events that are not shown to the player until they have assembled all the elements in a chapter -- and then materialize, say, at the end of it to complete the story arch.
Anyhow, keep up the great work and best of luck!