The protomolecule stuff drives the plot of the entire story. It's why the conflict happens, and how the characters end up in the middle of it, from the very fir

The protomolecule stuff drives the plot of the entire story. It's why the conflict happens, and how the characters end up in the middle of it, from the very first episode. And it keeps building on that all the way through the show and the books. The focus remains on humanity, but the alien stuff provides the motivation for the ongoing human response. Also, advanced alien tech in pretty much all science fiction follows Arthur C. Clarke's dictum about magic. Of course they're going to be able to do things humans don't understand. Do you really think we would be able to explain everything a billion+ year old civilization could do?