WASHINGTON — Federal prosecutors in Virginia are investigating a secret Turkish lobbying effort that once involved Michael T. Flynn, the former national security adviser, even as Mr. Flynn’s role in the special counsel’s investigation winds down, according to people familiar with the inquiry.
Robert S. Mueller III, the special counsel, had been handling the case and at some point referred it back to prosecutors in Alexandria, Va., who had originally opened the investigation, the people said. A veteran national security prosecutor is overseeing the case, and a grand jury has been empaneled to hear evidence.
Prosecutors for Mr. Mueller appeared to make reference to the investigation in documents released on Tuesday that enumerated Mr. Flynn’s cooperation in the Russia inquiry. The heavily redacted documents created an air of mystery about Mr. Flynn’s “substantial help” in several unspecified but continuing investigations. Prosecutors cited Mr. Flynn’s assistance as grounds for leniency when a judge sentences him on Dec. 18.
The Turkey case appears to fit as one of those inquiries because Mr. Flynn has direct knowledge of aspects under scrutiny. Prosecutors are examining Mr. Flynn’s former business partners and clients who financed a campaign against Fethullah Gulen, a cleric living in Pennsylvania whom the Turkish government has accused of helping instigate a failed coup.
Mr. Mueller’s prosecutors also mentioned Mr. Flynn’s help in their own investigation and in a third matter. Details about it were blacked out in court papers, so it was unclear whether Mr. Mueller’s team was describing additional details about its own inquiry, which also includes an examination of whether President Trump tried to obstruct it; citing investigations it has referred to other federal prosecutors’ offices, like the case in Manhattan against Mr. Trump’s personal lawyer, Michael D. Cohen; or describing a third investigation unknown to the public.
Mr. Flynn pleaded guilty last year to lying to F.B.I. agents about his contacts with Russia’s ambassador to Washington. Prosecutors asked Judge Emmet G. Sullivan of the United States District Court for the District of Columbia to sentence Mr. Flynn to little to no time in prison, noting that his military service of more than 33 years and public record “distinguish him from every other person” charged in the special counsel’s investigation.
Federal prosecutors had begun investigating Mr. Flynn after he wrote an op-ed for The Hill newspaper on Election Day 2016 attacking Mr. Gulen as a “radical Islamist” and a “shady Islamic mullah.” The prosecutors began examining whether Mr. Flynn was working as a paid lobbyist for Turkey.
Investigators later learned the op-ed was part of a larger effort by Mr. Flynn on behalf of Turkey. Mr. Flynn’s company was ultimately paid $530,000 to investigate Mr. Gulen by a company run by Ekim Alptekin, a Turkish businessman close to President Recep Tayyip Erdogan of Turkey.
In his first days as president, Mr. Trump asked the F.B.I. director James B. Comey that law enforcement officials drop the inquiry into Mr. Flynn. “I hope you can let this go,” the president said, according to Mr. Comey. The revelation helped prompt the appointment of Mr. Mueller to oversee the investigation into Russia’s election interference and whether any Trump associates conspired, as well as whether Mr. Trump himself tried to impede the inquiry.
As part of his work for Turkey, Mr. Flynn’s company sought to persuade members of Congress that Mr. Gulen ought to be extradited. Mr. Flynn also commissioned a lengthy dossier titled “Fethullah Gulen: A Primer for Investigators,” which was written by Thomas Neer, a former F.B.I. agent.
Mr. Mueller took over that aspect of the inquiry in 2017.
A spokesman for Mr. Mueller declined to comment. A spokesman for federal prosecutors in Virginia did not respond to a message seeking comment.
Many specifics of the Virginia investigation are unclear, but it could involve whether anyone associated with Mr. Flynn or his company failed to comply with the Foreign Agents Registration Act, the law requiring disclosures to the Justice Department about lobbying on behalf of foreign interests.
Mr. Flynn admitted to prosecutors last year that he had repeatedly violated that law. He had said he wrote the op-ed at his own initiative, concealing that he did so at the direction of Turkey. On Tuesday, prosecutors on Mr. Mueller’s team wrote that Mr. Flynn’s op-ed “was valuable to the Republic of Turkey’s efforts to shape public opinion.”
In 2017, Mr. Flynn and his business partner, Bijan Kian, filed additional lobbying disclosures acknowledging that the Gulen project “could be construed to have principally benefited the Republic of Turkey.” They detailed payments to roughly a dozen other people and firms associated with the Gulen project.
Prosecutors could also be investigating reports that Mr. Flynn discussed kidnapping the cleric as part of a plan to forcibly return him to Turkey. Mr. Flynn’s lawyer has denied his client considered kidnapping Mr. Gulen.
Last year, Mr. Alptekin told The New York Times that he wanted to hire a credible American company to lead an influence campaign against the Gulenists. He said Mr. Kian suggested Mr. Flynn’s company, Flynn Intel Group.
“You need independent work; you need research that is done by Americans,” Mr. Alptekin said in an interview.
Mr. Kian’s lawyer declined to comment.
Matthew Rosenberg contributed reporting.