The feds have been investigating
Here's how it went down:
Tor first popped onto the national security/federal crime radar, at least publicly, in June 2013, when a photo emerged of NSA leaker Edward Snowden's laptop, which features a Tor sticker.
Because Tor allows secret, anonymous and encrypted web browsing, it would be the perfect vehicle for someone like Snowden to store or transport secrets.
It's also perfect for criminals, as Business Insider revealed back in March.
Things came to a head in early August, when the FBI arrested a man who was allegedly trading child pornography via a Tor-hosted site called Freedom Hosting.
At that point, "dark web" sites began going offline as users figured out that as much as 50% of the Tor network had been compromised by the feds.
The fact that Ulbricht was still online, and operating Silk Road, through September, is therefore surprising. he had ample warning the feds were after him as far back as June.
In fact, as the indictment against him makes clear, the feds were on to Silk Road back in January 2011. Their investigation discovered him allegedly trying to hire a hitman to take care of an extortionist in March 2013.
The bottom line is that if you were doing anything illegal on Tor or Silk Road for the last three years, you may be screwed.