Federal prosecutors said on Friday that President Trump directed illegal payments to ward off a potential sex scandal that threatened his chances of winning the White House in 2016, putting the weight of the Justice Department behind accusations previously made by his former lawyer.
The lawyer, Michael D. Cohen, had said that as the election neared, Mr. Trump directed payments to two women who claimed they had affairs with Mr. Trump. But in a new memorandum arguing for a prison term for Mr. Cohen, prosecutors in Manhattan said he “acted in coordination and at the direction of” an unnamed individual, clearly referring to Mr. Trump.
In another filing, prosecutors for the special counsel investigating Russia’s 2016 election interference said an unnamed Russian offered Mr. Cohen “government level” synergy between Russia and Mr. Trump’s campaign in November 2015. That was months earlier than other approaches detailed in indictments secured by prosecutors.
And in a separate case on Friday, the special counsel accused Paul Manafort, Mr. Trump’s campaign chairman, of lying about his contacts with an individual they accuse of ties to Russian intelligence, and about his interactions with Trump administration officials after he was indicted on criminal charges.
Together, the filings laid bare the most direct evidence to date linking Mr. Trump to potentially criminal conduct, and added to an already substantial case that Russia was seeking to sway the 2016 election in his favor.
Mr. Trump sought on Friday to dismiss the news, wrongly claiming it “Totally clears the President. Thank you!”
The White House press secretary, Sarah Huckabee Sanders, was less unequivocal. “The government’s filings in Mr. Cohen’s case tell us nothing of value that wasn’t already known,” she said in a statement. “Mr. Cohen has repeatedly lied and as the prosecution has pointed out to the court, Mr. Cohen is no hero.”
She tried to distance Mr. Trump from the accusations against Mr. Manafort, who was convicted on financial fraud and conspiracy charges unrelated to his work for the Trump campaign. President Trump has repeatedly defended Mr. Manafort as a “brave man” and dangled the possibility of a pardon for his 10 felonies, likely to result in a prison term of at least 10 years.
The revelations came in dual filings by federal prosecutors for the Southern District of New York and by the special counsel, Robert S. Mueller III. Their work has intersected because both teams have charged Mr. Cohen with crimes, and he had sought to cooperate with both.
The prosecutors in New York mounted a scathing attack on Mr. Cohen’s character They rejected his plea to avoid a prison term, saying that he had “repeatedly used his power and influence for deceptive ends.”
They argued that he deserved a “substantial” prison term. Under sentencing guidelines, that would most likely to amount to about four years.
Mr. Cohen, 52, is to be sentenced next week for a guilty plea to campaign finance violations and financial crimes, and a second plea to lying to Congress about the extent of Mr. Trump’s business dealings in Russia.
Mr. Cohen’s crimes marked “a pattern of deception that permeated his professional life,” the Manhattan prosecutors wrote, saying that he did not deserve much leniency in exchange for cooperating with the government.
In a lengthy memo to the judge, William H. Pauley III, prosecutors wrote that Mr. Cohen was motivated by “personal greed” and had a “rose-colored view of the seriousness of the crimes.”
[Read the federal prosecutor’s memo ahead of Michael Cohen’s sentencing in Manhattan.]
They emphasized that Mr. Cohen had implicated the president in his guilty plea. “Cohen himself has now admitted, with respect to both payments, he acted in coordination with and at the direction of Individual-1,” the prosecutors wrote. “Individual-1” is how Mr. Trump is referred to in the document.
Mr. Cohen’s actions “struck a blow to one of the core goals of the federal campaign finance laws: transparency,” the prosecutors wrote, adding that he “sought to influence the election from the shadows.”
The special counsel’s prosecutors seemed to offer a more positive view of Mr. Cohen, saying he “has gone to significant lengths to assist the Special Counsel’s investigation.
They said Mr. Cohen had told them about a meeting that appeared to be the earliest-known contact between a Russian offering to help Mr. Trump’s campaign.
In November 2015, as discussions about a possible Trump Tower Moscow project were gaining momentum, Mr. Cohen told prosecutors he was approached by a Russian claiming to be a “‘trusted person’ in the Russian Federation,” who offered “synergy on a government level” with the Trump campaign, they said.
The individual, who was not named, pushed for a meeting between Mr. Trump and President Vladimir V. Putin of Russia. Such a meeting, he said, could have a “‘phenomenal’ impact ‘not only in political but in a business dimension as well.’”
Mr. Cohen told the special counsel’s team that he never followed up on the invitation.
Mr. Cohen has emerged as one of the biggest threats to Mr. Trump’s presidency, providing the special counsel’s office and prosecutors in Manhattan with material in dozens of hours of interviews. He met seven times with prosecutors for the special counsel, who are investigating Russian interference in the 2016 election and whether anyone tied to the Trump campaign conspired with Moscow’s efforts to influence the outcome of the vote.
In his first guilty plea in Manhattan, Mr. Cohen implicated Mr. Trump in hush-money payments to two women — Stormy Daniels, an pornographic film actress, and Karen McDougal, a former Playboy model — to conceal affairs they said they had with Mr. Trump. The prosecutors charged that the $130,000 payment to Ms. Daniels violated 2016 campaign finance law prohibitions against donations of more than $2,700 in a general election.
A $150,000 payment made by American Media Inc. to Ms. McDougal in late summer 2016 to buy the rights to her story constituted an illegal corporate donation to Mr. Trump’s campaign, the prosecutors said.
On Nov. 29, Mr. Cohen entered his second plea, revealing in court that Mr. Trump had been more involved in discussions over a potential deal to build a tower in Moscow than was previously known. He also said those discussions had continued until June 2016, well after Mr. Trump had clinched the Republican nomination and only five months before the election.
Mr. Trump’s interest in building a Trump Tower Moscow led Mr. Cohen to make numerous inquiries with Russian officials and other Kremlin-linked figures about the feasibility of the project, raising the possibility that the negotiations might have given the Russians leverage over Mr. Trump when he was running for president.
In Mr. Cohen’s own sentencing memo, filed on Nov. 30, his lawyers disclosed that their client had consulted with White House staff members and Mr. Trump’s “legal counsel” — without identifying the lawyer — as he prepared for his false congressional testimony.
Mr. Cohen said in court that he lied “out of loyalty” to Mr. Trump and to be consistent with his “political messaging.”
Mr. Cohen’s cases have been consolidated before Judge Pauley in Manhattan.
Mr. Cohen’s lawyers, Guy Petrillo and Amy Lester, have asked Judge Pauley to allow Mr. Cohen to avoid a prison sentence, citing his cooperation with Mr. Mueller even though he never signed a formal cooperation agreement.
They also portrayed him as a remorseful man whose life had been shattered by his relationship with Mr. Trump. They said Mr. Cohen had lost friends and professional relationships and wanted to confess his crimes, serve any sentence imposed and begin his life anew.
Under federal guidelines, Mr. Cohen faces about four to five years in the Manhattan case and up to six months in Mr. Mueller’s case. But the guidelines are not binding, and Judge Pauley will decide the final sentence.
Mr. Trump has accused Mr. Cohen of lying to prosecutors in hope of a lighter sentence, while trying to undermine public trust in the special counsel’s office and broadly, in the Justice Department. He kept up those attacks on Friday. In a series of Twitter messages, he derided Mr. Mueller as a friend of James B. Comey, the former F.B.I. director who said the president fired him in May 2017 after demanding “loyalty.”
Asked why the president was so upset about the special counsel, Roger J. Stone Jr., a friend and fellow critic of Mr. Mueller, said it had dawned on Mr. Trump that the inquiry is not going away, his lawyers’ promises notwithstanding. “He has finally figured out that this is about him,” he said. “I think he has finally woken up.”
Spurred on by the White House, House Republican lawmakers used their last days in control of the chamber’s majority to press Mr. Comey on Friday on what they claim is a pattern of abuse of power by the F.B.I. Mr. Comey reluctantly agreed to testify behind closed doors on Capitol Hill after the House Judiciary and Oversight and Government Reform committees agreed to release a public transcript of his testimony.
Lawmakers emerged frustrated that Mr. Comey had not been allowed to answer questions about classified matters involving the Mueller investigation, in which he is a central witness. Mr. Trump took up their complaints, tweeting that Justice Department lawyers had demonstrated “total bias and corruption at the highest levels of previous Administration.”
Emerging after six hours of questioning, Mr. Comey himself defended the F.B.I.’s actions in the Russia case, and accused Republicans of a continued preoccupation with the bureau’s handling during the 2016 campaign of an inquiry into Hillary Clinton’s use of a private email server.