NEW YORK—The Silk Road drug-trafficking trial seemed to be moving along swiftly last week, with testimony both Tuesday and Thursday containing big reveals about defendant Ross Ulbricht's strategy for proving his innocence.

Today, with jurors back after a five-day break, the action slowed to a crawl. Nearly the entire morning was consumed by government and defense lawyers arguing about what kind of evidence should be allowed in regarding theories about who else might have been Dread Pirate Roberts, or DPR, the pseudonymous boss of Silk Road, the largest online drug marketplace.

Much of the argument centered around the theory defense lawyer Joshua Dratel brought out on Thursday: that DPR could have been Mark Karpeles, the owner of the now-defunct Mt. Gox Bitcoin exchange. Karpeles, contacted by the media Thursday, has strenuously denied having any involvement in Silk Road.

In the mid-morning, US District Judge Katherine Forrest made a ruling from the bench that defense lawyer Joshua Dratel would have to avoid questioning the Homeland Security agent on the stand, Jared Der-Yeghiayan, about his "beliefs" and "suspicions." It's legitimate for the defense to pursue the idea of an "alternative perpetrator," she said, but such questioning should be limited to what Der-Yeghiayan did or saw himself, or learned during his investigation.

At one point during the morning discussion—only a portion of which happened in open court—Forrest asked Dratel directly if he intended to try to show that Mark Karpeles was the "real" DPR.

"My [position] is that he could be the real DPR," said Dratel. "Our theory is that Mr. Ulbricht created the site" but left within months, he said. "He didn't come back until the very end, and was not 'in' at the very end—not in the conspiracy. The fact that the evidence shows what he had on his laptop, at that time, we will explain."

In the afternoon, Forrest said she was going to strike much of Thursday's questioning about Der-Yeghiayan's "suspicions" about Karpeles from the record. Dratel complained vociferously.

"Now I have to go back and reconstruct," complained Dratel. "I'm not sure I can proceed."

"I'm done with this issue," said Forrest. "I'm not suggesting you should like it."

Meeting “Alternative Perpetrators”

As Der-Yeghiayan's cross-examination continued through the afternoon, the process became contentious, and slow. Prosecutor Serrin Turner objected to Dratel's questions as often as not. Forrest insisted that Dratel change the wording of his questions on many occasions, several times stepping in and asking Der-Yeghiayan questions about his direct knowledge, or lack thereof, herself.

By the end of the day, all the legal back-and-forth seemed to have little yield, for either side. A few specifics Dratel wanted in, such as details about what kind of offer Karpeles' lawyer made to the government, didn't get aired. But even as he complained bitterly about having information stricken from the record, most of Dratel's narrative got across to the jury. Prosecutors confirmed the basics when they questioned Der-Yeghiayan at the end of the day.

It's clear that Karpeles was once under investigation, but that investigation ended. By early 2014—after the arrest of Ross Ulbricht—Der-Yeghiayan was able to spend a few weeks reading Karpeles' emails, which he acquired with a search warrant.

Karpeles "controlled a lot of websites," Dratel said, including SilkRoadMarket.org, a website that served as the open-Internet advertisement for the real Silk Road, which was hidden on the Tor-only part of the Internet. Der-Yeghiayan said Karpeles merely hosted SilkRoadMarket.org through his hosting company, KalyHost, which accepted payment for the site in bitcoin, from a customer apparently using a fake name.

Dratel drew out more circumstantial evidence that could be seen as pointing to Karpeles, or another DPR more generally. For instance, he asked Der-Yeghiayan about the meteoric rise of bitcoin values during the Silk Road investigation; the price rose from just a few dollars per bitcoin in 2011, to more than $250 in early 2013, settling at around $100 per bitcoin when Ulbricht was arrested. Dratel also pointed out that a Silk Road 2.0 was up less than two months after Ulbricht's arrest. And he drew out a line of questioning confirming there was tension between the various offices investigating Silk Road, with Der-Yeghiayan's Chicago office sometimes disagreeing with steps taken by federal agents in New York and Baltimore.

Finally, Dratel has also made clear there's at least one more "alternative perpetrator" he wants to talk about in addition to Karpeles. He briefly asked about Der-Yeghiayan looking into a Canadian citizen named "Anand Athavale," noting he owned many websites and had computer expertise. The questioning about Athavale didn't go much beyond that, though, and it's not at all clear what links Dratel intended to draw there. Der-Yeghiayan admitted looking at Athavale's LinkedIn page, but that's it.

The cross-examination ended at around 4:30pm. The day ended with Turner getting in about 25 minutes of "re-direct" testimony. Der-Yeghiayan will still be on the stand tomorrow, although not for long.