Authorities took their case to a grand jury in Baltimore and obtained a sealed indictment May 1 charging Dread Pirate Roberts with drug offenses, attempted witness murder and murder for hire. The agents had charges, but they still did not know who Dread Pirate Roberts really was.
By that point, the Maryland agents were working with the New York FBI office. The two teams began to try to figure out what they each had.
"Everyone had that little piece of the puzzle, then it was time to sit at the table and put it together," Eisert said, a process carried out in a series of conferences and phone calls.
They also continued to ratchet up pressure on Silk Road.
In May and July, authorities in Maryland announced that they had seized the assets of a company called Mt. Gox, the largest exchanger of Bitcoins, alleging that it had violated currency trading rules.
Bitcoin exchanges are a critical link between the online wealth being accumulated by Silk Road users and the real world, and the seizure was also part of a bid to smoke out Dread Pirate Roberts. Those cases are still open; Mt. Gox did not respond to a request for comment and has responded in court.
Tuggle said Dread Pirate Roberts began looking for ways to "insulate himself," and soon moved to obtain fake identity documents so he could rent servers under assumed names, according to court documents in Ulbricht case.
In July, Customs and Border Patrol intercepted documents on the way to his San Francisco home at the Canadian border, according to the charging papers.
At the end of the month, HSI agents turned up at the address and finally, they were face to face with the man they believed to be Dread Pirate Roberts.
At around the same time, the FBI made another major step forward, obtaining a complete image of a Silk Road server hosted in another country. Authorities said that image gave them a look at all messages and transactions on the site.
How the FBI tracked down the server, which should have been masked in the Tor system, and exactly how critical it was to unmasking Ulbricht are still unexplained. The FBI New York office declined to answer questions for this article.
"There are a number of theories flying around, some even include the use of [National Security Agency] exploit tools to hack into Silk Road," said Runa A. Sandvik, a researcher at the Tor Project. "I am hoping we learn more during Ulbricht's trial."
Authorities also found a LinkedIn page for Ulbricht. They wrote in the charges against him that it showed clues to his hidden life, including that he was "creating an economic simulation" believed to be Silk Road.
Ulbricht was arrested in October. Silk Road was seized and shut down, and charges were announced against a number of other users of the site.
Among them was Green, who pleaded guilty to a drug charge in Baltimore this month.