On Nov. 21, the United States attorney’s office in Manhattan wrote to the judge, asking for permission to tell the defense about the San Francisco investigation into Mr. Force and seeking an order prohibiting the defense from disclosing its existence.

The letter contended Mr. Force had “played no role” in the Manhattan-based investigation of Mr. Ulbricht; rather, the agent had been part of a separate inquiry in Baltimore that resulted in the filing of charges there against Mr. Ulbricht.

The prosecutors argued that the Force investigation was not “in any way exculpatory as to Ulbricht or otherwise material to his defense” — the kind of information the government would be required to turn over — but added that they were providing the information “in an abundance of caution.”

On Dec. 1, Judge Forrest granted the government’s request, and Mr. Ulbricht’s lawyers were told about the investigation. In early December, the defense responded with its own sealed arguments that the information about the Force investigation was both material and potentially exculpatory, and should be unsealed and admitted at trial.

“We thought it was relevant and helpful to our defense, which was that other people had access to the Silk Road site and a motivation to frame Ross Ulbricht,” Mr. Ulbricht’s lawyer, Joshua L. Dratel, said on Wednesday.

In court filings, the prosecutors, Mr. Howard and Serrin Turner, affirmed their opposition to disclosing the information to the jury, calling it “irrelevant and inflammatory,” and saying it tended to bolster Mr. Ulbricht’s guilt, not his innocence. They said that in the Manhattan case, the government “has not relied on and is not offering any evidence” from the Baltimore investigation.

Mr. Dratel, at the Dec. 15 hearing, argued that without the information, “we’re going to be fighting this fight with hands tied behind our backs.”