How are discoveries made in microbiology?

I have likely asked this before, but it still remains a mystery to me. How do you take a bunch of goop from some organism and identify the various molecular components, figure out their structure and determine how they interact? I have seen detailed animations of how viruses invade a cell and use the cell’s machinery to reproduce. To me, being able to figure this out seems like magic.

I don’t want a low level description, just something at a relatively high level that outlines the sequence of procedures used.