If this sounds complicated, just focus on this: naked short selling, in essence, is selling stock you do not have. If you don't have to actually locate and borrow stock before you short it, you're creating an artificial supply of stock shares.
In this case, that resulted in absurdities like the following disclosure in this document, in which a Goldman executive admits in a 2006 email that just a little bit too much trading in Overstock was going on: "Two months ago 107% of the floating was short!"
In other words, 107% of all Overstock shares available for trade were short - a physical impossibility, unless someone was somehow creating artificial supply in the stock...
How they did this is ingenious, elaborate, and complex, and we'll get into it more at a later date. In the meantime, this document all by itself shows numerous executives from companies like Goldman Sachs Execution and Clearing (GSEC) and Merrill Pro talking about a conscious strategy of "failing" trades - in other words, not bothering to locate, borrow, and deliver stock within the time alotted for legal settlement.
Link
Most people would call selling what you don't own fraud (e.g. the canonical Brooklyn Bridge salesman). Add this to front running and it's other crimes and one wonders if the company's continued existence has anything to do with it's former employees being in most of the government's top financial regulation positions. If so, is our government effectively being run by criminal organizations?