Flynn and his company were paid $530,000 for their Turkey-related work.
The indictment says that Flynn, identified as "Person A," and Kian founded a company that offered clients services based on Flynn's "national security expertise."
Kian and Alptekin then allegedly secretly conspired to influence American politicians and public opinion about Gulen, when the cleric's extradition was being sought by Turkey. The Justice Department was resisting that request.
According to the indictment, Kian and Alptekin worked at the direction of the government of Turkey. But they tried to conceal that by having Alptekin's firm, rather than the Turkish government, serve as the client of Flynn's company, according to court documents.
In his subsequent op-ed for The Hill, Flynn labeled Gulen a "shady Islamic mullah," and "a radical Islamist" — and compared him to Iran's Ayatollah Khomeini and to Osama bin Laden.
"We should not provide him safe haven," Flynn wrote of Gulen. "In this crisis, it is imperative that we remember who our real friends are."
The op-ed was published Nov. 8, 2016 — the same day as the presidential election — and was a direct result of the conspiracy, according to the indictment.
On Nov. 4, 2016, Kian emailed Alptekin about the op-ed, saying, "I just left [Person A]. The arrow has left the bow! ... This is a very high profile exposure one day before the election," according to the indictment. Attached to that email was a draft of Flynn's op-ed.
The op-ed contained the same description of Khomeini sitting under an "apple tree" that Kian had made in emails and a draft version of the op-ed, the indictment noted.
After the 2016 election, Alptekin told NBC News that he was not affiliated with the Turkish government, and that his hiring of the Flynn Intel Group had nothing to do with the Turkish government.
Flynn served as Trump's national security advisor for less than a month. He resigned under pressure in February 2017, after lying to Vice President Mike Pence about the nature of his contacts with Kislyak.
The indictment says that while Flynn was national security advisor, and for a month or so thereafter, lawyers for Flynn's firm tried to determine if the firm and its employees needed to register as agents of foreign governments based on their work in the effort to discredit Gulen.
Kian and Alptekin "knowingly provided false information to [Flynn's firm's] attorneys in an effort to hide from the attorneys — and ultimately from the [Justice Department's Foreign Agents Registration Act] unit — the involvement of Turkish government officials in the project," the indictment says.
If convicted, Kian faces a maximum of 15 years in prison, according to a Justice Department press release. Alptekin's charges add up to a maximum sentence of 35 years in prison.
Read the full indictment below: