Flynn has been charged for his involvement with alleged Russian meddling in the 2016 United States presidential election.
The plan was developed at the height of the 2016 election campaign when Flynn was advising then-candidate Trump on foreign and security policy.
Turkey's President Recep Tayyip Erdogan has been lobbying to have his enemy Gulen, a 75-year-old Islamic preacher who lives in Pennsylvania, extradited back to Turkey.
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"Although the Government of Turkey directed the work through Alptekin, the defendants sought to hide Turkey's involvement in the efforts to discredit the Turkish citizen", the indictment reads.
The probe into Flynn and his now defunct lobbying and consulting business had been handled previously by Special Counsel Robert Mueller as part of his investigation into possible collusion between Russian Federation and the Trump campaign.
After the op-ed was published, the DOJ's FARA unit contacted Flynn to investigate the circumstances surrounding the publication.
Flynn admitted one count of lying to the FBI in a plea deal which led to him providing "substantial" information to Special Counsel Robert Mueller's investigation into Russian Federation meddling in the 2016 election.More news: Isha Ambani-Anand Piramal Wedding: First Pics of B-Town Celebs
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Rafiekian founded the Flynn Intel Group with Flynn to offer advisory services based on Flynn's national security expertise.
Kian's attorney Robert Trout declined to comment on the matter. He has previously denied any wrongdoing and said he directed the lobbying on his own. The pair sought to hide that the work was, in fact, directed by the Turkish government, federal prosecutors said.
"Ekim remains adamant that he - and he alone - ultimately moved forward with hiring FIG, paying them, and directing their work", Molly Toomey said.
The Turkey case against Kian and Alptekin, though, is being handled by Assistant U.S. Attorneys James Gillis and Evan Turgeon in the Eastern District of Virginia, not the special counsel. Prosecutors say that Turkish officials approved the budget for the $600,000 lobbying contract and received regular progress reports.
According to the indictment, Flynn, Kian and Alptekin's secret lobbying effort against Gulen, initially dubbed the 90-day "Truth Campaign" and later named "Project Confidence", began in late July 2016, after the U.S. Justice Department rejected the Turkish government's request to extradite Gulen from the United States earlier that year. But prosecutors say he also received portions of the money as "kickbacks" arranged by Kian. He said in a phone interview that he hired Flynn to help secure a deal with Ratio Energy, an Israeli energy company.
Alptekin, 41, maintained that he was Flynn's client and not Turkey, a spokesperson said.
Flynn's op-ed was published in The Hill on November 8, the day Trump was elected. Prosecutors trace a line comparing the Ayatollah Khomenei's pre-revolutionary days meditating under an "apple tree" in France to Gulen's spiritual refuge in Pennsylvania from an August 4 email that Kian sent Flynn to the final draft, published in November. The indictment notes that Flynn's column uses identical or very similar language to that prepared by Kian in a draft op-ed. "He claimed to be a man of God who wanted to be a dictator".