The candidate he was advising last fall was running on a platform of America First.
The client he was working for last fall was paying him more than $500,000 to put Turkey first. Michael T. Flynn, who went from the campaign trail to the White House as President Trump’s first national security adviser, filed papers this week acknowledging that he worked as a foreign agent last year representing the interests of the Turkish government in a dispute with the United States.
His surprising admission, coming more than four months after the election, raised further questions about the rise and fall of a presidential confidant who was forced to resign after 24 days in office for withholding the full story of his communications with Russia’s ambassador.
Even now, out of government and out of favor, Mr. Flynn and his contact with foreign figures presented a new headache for a White House eager to move on.
Mr. Flynn, a retired Army lieutenant general, registered as a lobbyist last year but did not file papers with the Justice Department registering as a foreign agent, providing a fuller understanding of his role, until Tuesday.
While he did not work directly for the Turkish government, the firm that hired him, Inovo, is owned by a Turkish-American businessman with links to leaders in Ankara and asked him to work on an important issue.
The White House said that Mr.Trump did not know that Mr. Flynn was acting as a foreign agent when Mr. Trump appointed him national security adviser, a position that gave him access to classified meetings and materials.
But a person briefed on the matter, who insisted on anonymity to describe private conversations, said Mr. Flynn’s lawyer contacted a lawyer for Mr. Trump’s transition team before the inauguration to ask whether Mr. Flynn should register given his work for Inovo.
The transition lawyer offered no advice, saying it was up to Mr. Flynn. After the inauguration, the person said, Mr. Flynn and his lawyer each raised it again with a White House lawyer, only to be told once more it was up to him. Mr. Flynn had no comment on Friday.
His lawyer wrote the Justice Department that Mr. Flynn decided to register retroactively “to eliminate any potential doubt.” The White House said its lawyer considered it a private decision and saw no reason to intervene. “It’s not a question of raising a red flag,” said Sean Spicer, the White House press secretary.
“It’s a question of whether or not they gave him the advice that they are supposed to, which is it is not up to them to make decisions as to what you need to do or not do.” Vice President Mike Pence, who was upset that Mr. Flynn had misled him about the conversation with the Russian ambassador that got him dismissed, seemed less forgiving.
News reports on the matter were “the first I heard of it,” the vice president said during an interview on Fox News Thursday night, “and I think it is an affirmation of the president’s decision to ask General Flynn to resign.”
Throughout the campaign, Mr. Flynn positioned himself as someone willing to call out a national security establishment that was too corrupt to keep America safe. When former colleagues criticized him for becoming overtly partisan, he shot back by castigating them for using their titles to enrich themselves by joining corporate boards.
In an interview in October, Mr. Flynn insisted that he had eschewed financial rewards to follow his political convictions and join the Trump campaign. “I would love to be making some money,” he said. “I wish I could stop what I’m doing.”
On behalf of his firm, the Flynn Intel Group, Mr. Flynn signed a contract on Aug. 9 with Inovo, a Dutch firm owned by Ekim Alptekin, the chairman of the Turkish-American Business Council. Mr. Flynn’s firm was to receive $600,000 for 90 days of work. His initial registration as a lobbyist last year indicated he would receive less than $5,000 for lobbying, although that presumably indicates that he did not define most of the services he would provide Mr. Alptekin as lobbying under the law.
Mr. Alptekin has links to the government of Turkey’s president, Recep Tayyip Erdogan, which has engaged in a political crackdown after surviving a military coup attempt in July. In documents disclosed by the anti-secrecy group WikiLeaks, Mr. Alptekin emailed frequently with Egemen Bagis, the former Turkish minister for European Union affairs.
In one email in 2013, Mr. Alptekin sent an article from The Wall Street Journal to Mr. Bagis, who then forwarded it to Berat Albayrak, Mr. Erdogan’s son-in-law and now the country’s energy minister.
Mr. Flynn was assigned to investigate Fethullah Gulen, a Turkish cleric who lives in Pennsylvania and was blamed by Mr. Erdogan for helping instigate the failed coup. Mr. Erdogan has demanded the United States extradite Mr. Gulen, which the Obama administration refused to do.
The forms filed this week indicate that Mr. Flynn’s firm was “to perform investigative research” on Mr. Gulen and “develop a short film piece on the results of its investigation.” In the end, the video was never completed, and Mr. Flynn’s firm received $530,000 before the contract terminated in November.
But on Election Day, Mr. Flynn published an op-ed article in The Hill, a newspaper serving Congress, calling Mr. Gulen “a shady Islamic mullah” and “radical Islamist.” “To professionals in the intelligence community, the stamp of terror is all over Mullah Gulen’s statements,” he wrote.
“Gulen’s vast global network has all the right markings to fit the description of a dangerous sleeper terror network. From Turkey’s point of view, Washington is harboring Turkey’s Osama bin Laden.”
The forms said Mr. Flynn decided to write the piece “on his own initiative” and not at Inovo’s request, although they said that he shared a draft of it with Inovo before it was published.
The Hill appended a note to the online version of the piece after this week’s filing: “Neither General Flynn nor his representatives disclosed this information when the essay was submitted.” During the course of the work, Mr. Alptekin introduced Mr. Flynn to Foreign Minister Mevlut Cavusoglu and Mr. Albayrak, the president’s son-in-law, in New York on Sept. 19, the forms said.
In a letter to the Justice Department this week, Mr. Flynn’s lawyer said that he did not initially register as a foreign agent because the firm that hired him was not a foreign government.
But the lawyer, Robert K. Kelner, said Mr. Flynn had decided to register after the fact because “the engagement could be construed to have principally benefited the Republic of Turkey.” This week, Mr. Alptekin disputed the notion that he hired Mr. Flynn to influence the next president.
“When I engaged Flynn Co. polls showed 85% likelihood of Hillary winning,” he wrote on Twitter after the filings.
“If intention was to lobby USG I would have hired Podesta like Gulen,” he added, referring to the United States government and Tony Podesta, a prominent Washington lobbyist and brother of John D. Podesta, who was Mrs. Clinton’s campaign chairman. But the filings this week contradict past assertions by Mr. Alptekin, who told The New York Times in an interview after the November election that the contract with Mr. Flynn was worth “tens of thousands of dollars, not hundreds of thousands of dollars.”
In the same interview, he said that Mr. Flynn “never consulted with me” about the op-ed article in The Hill and that he “would have advised against it.”
Mr. Alptekin repeated the latter assertion even after the filings this week. “For the record: nobody remotely linked to the Gov. of Turkey knew about Gen. Flynn’s article in advance and I wasn’t consulted either,” he wrote on Twitter.
Mr. Flynn opened the Flynn Intel Group in October 2014, two months after he was forced out as director of the Defense Intelligence Agency. The business was opaque, making little public, not even an address. When a reporter went looking for it last fall, he tracked it down to an Alexandria, Va., office building operating out of the nondescript headquarters of another firm, called the White Canvas Group.
In the interview in October, Mr. Flynn offered only a vague description of the firm.
He said he had clients in Japan and the Middle East and that he worked on cybertraining, aviation operations and energy business.
The firm was shuttered after the election when Mr. Flynn was headed for the White House.