...It's interesting that the "Deep Web" was originally built by the U'S, military (at least this is what the article claims). The TOR project is currently administered by a nonprofit organization based in Cambridge, Mass., and sponsored by a diverse array of organizations including Google and the Knight Foundation. But, as recently as 2011, 60% of its funding still came from the U.S. Government.
The corruption of the Deep Web began not long after it was built. As early as 2006, a website that came to be known as The Farmer's Market was selling everything from marijuana to ketamine.
Most of the Time Magazine article describes a website known as: "The Silk Road",...which, for 2 and a half years acted as an Amazon-like clearinghouse for illegal goods, providing almost a million customers with $1.2 Billion worth of contraband. Most of the second half of the article describes the efforts of the FBI to locate and prosecute the individual running Silk Road.
Here is a quote from the article: "Most people who use the Deep Web aren't criminals. But some prosecutors and government agencies think that Silk Road was just the thin edge of the wedge and that the Deep Web is a potential nightmare, an electronic haven for traffickers, child pornographers, human traffickers, forgers, assassins and peddlers of state secrets and loose nukes. The FBI, the DEA, the ATF and the NSA, to name a few, are spending tens of millions of dollars trying to figure out how to crack it."