it was good old police undercover infiltration work (while waiting patiently instead of jumping immediately on the chance just to break everything up but without really arresting everybody involved) and the cooperation of the host of the site (most of the TOR webservers are in fact on western hosts)
"Authorities said that they were able to arrest Benthall after an undercover Homeland Security agent was able to gain the trust of Silk Road 2.0′s administrators and received access to “private, restricted areas” of the site reserved for its leaders. Through that operation, the agent said he was able to interact directly with Defcon.
That agent detailed his investigation in full in the criminal complaint against Benthall, noting that he had attained moderator privileges on a forum that formed after the closure of the original Silk Road site. On that forum, the agent was able to see discussions between users who toyed with the idea of creating a successor site.
In May, agents were able to locate the server hosting Silk Road 2.0 in a foreign country, tracing alleged ownership back to Benthall. As the agent wrote: “Based on a review of records provided by the service provider for the Silk Road 2.0 Server, I have discovered that the server was controlled and maintained during the relevant time by an individual using the email account firstname.lastname@example.org.”
well once you get the emailaddress you get anything else, why didn't the guy use a tor emailserver - didn't trust it or lazy - those amateur undercover anonymous activists and wouldbe online gangsters don't really have the knowledge or guts or time to keep their identity anonymous (and so they get caught)
and these are the main targets for the next operation because not all of the top five illegal bazaars have been taken offline
"A study by the non-profit Digital Citizens Alliance in September found that the six most popular Tor-based markets by total product listings were Silk Road 2, Agora, Evolution, Pandora, Andromeda, and BlueSky. Operation Onymous captured fully half of those top sites. But Agora, Evolution and Andromeda remain online and will likely absorb many of the refugee buyers and sellers from the law enforcement busts. In fact, Agora had already passed the Silk Road in total product listings with more than 16,000 mostly-illegal offerings, and the fast-growing marketplace Evolution was already on pace to soon take the second place spot in the underground economy. via Andy Greenberg/WIRED
but there are more operations to come because the police forces have set up a central command center for this kind of operations
"The operation fits the objectives of Project ITOM (Illegal Trade in Online Marketplaces), an official Dutch initiative, supported by the European Union, to enhance cooperation between law enforcement and judicial authorities in an effort to hinder the development of online marketplaces.
and the goals of this operation are
what did you think that you could sell freely for millions of drugs online and that no police force would come to get you one way or another ?
if you read the chart above than you could also have - as a police officer - the following idea - let's shut down all those email and other contactservices on TOR so that they are obliged to use 'public' services to make contact - or set up honeypot torservices with email and so on so you can attract them, follow them and arrest them in another sweep - and if you do it you have another big advantage - that is that people won't trust any TORservice anymore because they don't know if it is a real one or a honeypot from the police (palace of mirrors)
and that is just the biggest problem or advantage of TOR for undercover operations - there is no way any user can know if a service if really anonymous, secure, hosted in an unreachable country or relayed with a real and not a fake relay tor server, operated by the police or not because otherwise TOR wouldn't be as anonymous
By the way the Belgians DO NOT PARTICIPATE in this operation - for now (fccu ? how come ? You have some of the best specialists on TOR it is being said)