But Durham used a 27-page indictment to lay out a far more expansive tale, one in which four computer scientists who were not charged in the case “exploited” their access to internet data to develop an explosive theory about cyberconnections in 2016 between Donald Trump’s company and a Kremlin-linked bank — a theory, he insinuated, they did not really believe.

Durham’s version of events set off reverberations beyond the courtroom. Trump supporters seized on the indictment, saying it shows that suspicions about possible covert communications between Russia’s Alfa Bank and Trump’s company were a deliberate hoax by supporters of Hillary Clinton and portraying it as evidence that the entire Russia investigation was unwarranted.

Emails obtained by The New York Times and interviews with people familiar with the matter, who spoke on the condition of anonymity to discuss issues being investigated by federal authorities, provide a fuller and more complex account of how a group of cyberexperts discovered the odd internet data and developed their hypothesis about what could explain it.

At the same time, defense lawyers for the scientists say it is Durham’s indictment that is misleading. Their clients, they say, believed their hypothesis was a plausible explanation for the odd data they had uncovered — and still do.

The Alfa Bank results “have been validated and are reproducible. The findings of the researchers were true then and remain true today; reports that these findings were innocuous or a hoax are simply wrong,” said Jody Westby and Mark Rasch, lawyers for David Dagon, a Georgia Institute of Technology data scientist and one of the researchers whom the indictment discussed but did not name.

Steven Tyrrell, a lawyer for Rodney Joffe, an internet entrepreneur and another of the four data experts, said his client had a duty to share the information with the FBI and that the indictment “gratuitously presents an incomplete and misleading picture” of his role.

Durham’s indictment provided evidence that two participants in the matter — Joffe and Michael Sussmann, the cybersecurity lawyer accused of falsely saying he had no client when he brought the findings of the researchers to the FBI — interacted with the Clinton campaign as they worked to bring their suspicions to journalists and federal agents.

A spokesperson for Durham declined to comment. The special counsel’s office issued a fresh grand jury subpoena to Sussmann’s former law firm, Perkins Coie, sometime after Sussmann was indicted Sept. 16, in a development first reported Thursday by CNN and confirmed by a person familiar with the matter. It is unclear whether the subpoena pertained to Alfa Bank or whether Durham has finished his investigation into that case.

Durham uncovered law firm billing records showing that Sussmann, who represented the Democratic National Committee on issues related to Russia’s hacking of its servers, had logged his time on the Alfa Bank matter as work for the Clinton campaign. Sussmann has denied lying to the FBI about whom he was representing in coming forward with the Alfa Bank data, while saying he was representing only Joffe and not the campaign.

Durham also found that Joffe had met with one of Sussmann’s law firm partners, Marc Elias, who was then the Clinton campaign’s general counsel, and researchers from Fusion GPS, an investigative firm Elias had commissioned to scrutinize Trump’s purported ties to Russia. Fusion GPS drafted a paper on Alfa Bank’s ties to the Kremlin that Sussmann also provided to the FBI.

In the heat of the presidential race, Democrats quickly sought to capitalize on the research. On Sept. 15, four days before Sussmann met with the FBI about the findings, Elias sent an email to the Clinton campaign manager, Robbie Mook; its communications director, Jennifer Palmieri; and its national security adviser, Jake Sullivan, whose subject line referred to an Alfa Bank article, the indictment said.

Six weeks later, after Slate ran a lengthy article about the Alfa Bank suspicions, the Clinton campaign pounced. Clinton’s Twitter feed linked to the article and ran an image stating the suspicions as fact, declaring, “It’s time for Trump to answer serious questions about his ties to Russia.”

The FBI, which had already started its Trump-Russia investigation before it heard about the possible Trump-Alfa connections, quickly dismissed the suspicions, apparently concluding the interactions were probably caused by marketing emails sent by an outside firm using a domain registered to the Trump Organization. The report by the Russia special counsel, Robert Mueller, ignored the issue.

The data remains a mystery. A 2018 analysis commissioned by the Senate, made public this month, detailed technical reasons to doubt that marketing emails were the cause. A Senate report last year accepted the FBI’s assessment that it was unlikely to have been a covert communications channel but also said it had no good explanation for “the unusual activity.”

Whatever caused the odd data, at issue in the wake of the indictment is whether Joffe and the other three computer scientists considered their own theory dubious and yet cynically went forward anyway, as Durham suggests, or whether they truly believed the data was alarming and put forward their hypothesis in good faith.

Earlier articles on Alfa Bank, including in Slate and The New Yorker, did not name the researchers and used pseudonyms like “Max” and “Tea Leaves” for two of them. Durham’s indictment did not name them, either.

But three of their names have appeared among a list of data experts in a lawsuit brought by Alfa Bank, and Trump supporters have speculated online about their identities. The Times has confirmed them, and their lawyers provided statements defending their actions.

The indictment’s “Originator-1” is April Lorenzen, chief data scientist at the information services firm Zetalytics. Her lawyer, Michael Connolly, said she has “dedicated her life to the critical work of thwarting dangerous cyberattacks on our country,” adding, “Any suggestion that she engaged in wrongdoing is unequivocally false.”

The indictment’s “Researcher-1” is another computer scientist at Georgia Tech, Manos Antonakakis. “Researcher-2” is Dagon. And “Tech Executive-1” is Joffe, who in 2013 received the FBI Director’s Award for helping crack a cybercrime case and retired this month from Neustar, another information services company.