Even as the special counsel, Robert S. Mueller III, submitted his confidential report to the Justice Department on Friday, federal and state prosecutors are pursuing about a dozen other investigations that largely grew out of his work, all but ensuring that a legal threat will continue to loom over the Trump presidency.
Most of the investigations focus on President Trump or his family business or a cadre of his advisers and associates, according to court records and interviews with people briefed on the investigations. They are being conducted by officials from Los Angeles to Brooklyn, with about half of them being run by the United States attorney’s office in Manhattan.
Unlike Mr. Mueller, whose mandate was largely focused on any links between the Trump campaign and the Russian government’s interference in the 2016 presidential election, the federal prosecutors in Manhattan take an expansive view of their jurisdiction. That authority has enabled them, along with F.B.I. agents, to scrutinize a broader orbit around the president, including his family business.
Mr. Trump told The New York Times in 2017 that investigations into his family’s finances, beyond any relationship to Russia, would cross a red line, and last year he privately asked the former acting attorney general, Matthew G. Whitaker, if someone he viewed as loyal could be put in charge of the investigations at the Manhattan office, The Times reported last month.
Some of those federal investigations in the Manhattan office, known as the Southern District of New York, grew out of its case against Michael D. Cohen, the president’s former lawyer and fixer. The inquiry into Mr. Cohen was turned over to the Manhattan federal prosecutors early last year after Mr. Mueller’s office spent months investigating him, court records unsealed this week show.
By dint of its location in Manhattan, a few miles south of the Trump Organization’s offices on Fifth Avenue, the Southern District was a natural landing spot for the Cohen case.
Situated in a drab, nine-story Brutalist-style building nestled among the federal courthouse, Police Headquarters and the Church of St. Andrew, the office has a history of high-profile prosecutions and personnel. From the espionage trial of the Rosenbergs in the early 1950s to the case of an Egyptian sheikh who plotted to bomb city landmarks four decades later, the office’s prosecutions have started the careers of judges, F.B.I. directors and even a New York City mayor.
Since Mr. Cohen pleaded guilty in August to helping arrange hush money payments to women who said they had affairs with Mr. Trump, the prosecutors have focused on what role the Trump Organization and its executives, including its longtime chief financial officer, may have played in the scheme, according to people briefed on the matter.
Mr. Cohen, who is scheduled to begin serving a three-year prison sentence in May, has assisted the prosecutors with that inquiry as well as a separate investigation into the president’s inaugural committee, the people said.
The prosecutors have also examined information brought by Mr. Cohen that he hopes will reduce his sentence, the people said, including whether Mr. Trump’s lawyers considered offering him a presidential pardon to keep him quiet and whether the Trump Organization possibly inflated insurance claims several years ago.
At this point, it is unclear whether anyone will be charged with a crime. Some of the investigations involve allegations that may be too old to be prosecuted. Yet taken together, the investigations show that the prosecutorial center of gravity has shifted from Mr. Mueller’s office in Washington to New York.
“The important thing to remember is that almost everything Donald Trump did was in the Southern District of New York,” said John S. Martin Jr., a retired federal judge who was the United States attorney in the Southern District during the Carter and Reagan administrations.
“He ran his business in the Southern District. He ran his campaign from the Southern District,” Judge Martin said. “He came home to New York every night.”
In an interview that aired on Friday morning, Mr. Trump told Maria Bartiromo of Fox Business Network that his lawyers were perplexed by reports that he faces multiple investigations.
“I said to my lawyers, ‘Are we being looked at here?’” Mr. Trump said, adding that his lawyers “don’t even know what people are talking about.”
James M. Margolin, a spokesman for the Southern District, declined to comment, as did the Trump Organization.
The precise number of federal investigations around the country that have grown out of the special counsel’s work remains unknown because such inquiries are conducted in secret. But the special counsel’s office farmed out strands of its inquiry to at least three other United States attorneys’ offices, including in Brooklyn, the District of Columbia and the Eastern District of Virginia.
People briefed on the federal investigations said the prosecutors in Brooklyn have raised questions about donations to the Trump inaugural committee, which was chaired by Thomas J. Barrack, a longtime friend of Mr. Trump. They have been examining Mr. Barrack’s ties to the Middle East, among other matters, according to the people briefed on the work.
Federal prosecutors in the District of Columbia will handle the prosecution of the Trump political adviser Roger J. Stone Jr., who was charged as part of Mr. Mueller’s investigation. And the Justice Department continues to investigate the business and political dealings of Elliott Broidy, a top fund-raiser for Mr. Trump’s campaign and inauguration, who tried to use his access to the Trump team to boost his businesses. Federal investigators in Los Angeles have also taken part in the inquiry and have raised questions about the inauguration, according to people briefed on the matter.
Separately, state authorities in New York are pursuing several investigations focused on the president, his associates and his business. Those matters include a mortgage fraud case against Mr. Trump’s former campaign chairman, Paul J. Manafort, as well as civil inquiries into the Trump Organization’s insurance practices, real estate deals, and whether the family’s charitable foundation violated tax laws.
As for the Southern District, it is known to move aggressively — more so than some other offices — to stake a claim to new investigations based on tips from cooperating witnesses and other sources. In this instance, it appears to be leading some of the most sensitive spinoffs — ones with the potential to directly affect Mr. Trump’s business, his inaugural committee and possibly himself.
In the hush money investigation, the Southern District prosecutors have already implicated the president, claiming in a court filing that Mr. Cohen “acted in coordination with and at the direction of” Mr. Trump. While the prevailing view at the Justice Department is that a sitting president cannot be indicted, the prosecutors in Manhattan could consider charging him after he leaves office, particularly if he does not win re-election and is a private citizen before the legal deadline to file charges expires.
The investigation into the Trump inaugural committee partly grew out of a recording that F.B.I. agents seized when they raided Mr. Cohen’s home and office. On the recording, Mr. Cohen is heard discussing potential irregularities with one of the main contractors for the inauguration. The Southern District is investigating, among other things, whether the committee made false filings with the Federal Election Commission and received illegal donations from foreign nationals, a subpoena from the investigation shows.
In addition, the Southern District took on two investigations stemming from the cases against Mr. Manafort, who was prosecuted by Mr. Mueller’s office and was recently sentenced to more than seven years in prison for a litany of crimes.
In one of the investigations, the prosecutors are weighing charges against the officer of a bank that Mr. Manafort has acknowledged defrauding, according to people briefed on the matter.
In the other, Mr. Mueller’s team referred investigations involving three firms that worked with Mr. Manafort — the lobbying firms Mercury Public Affairs and Podesta Group, and the law firm Skadden, Arps, Slate, Meagher & Flom — to the Southern District for potential prosecution under the Foreign Agents Registration Act.
Since then, Skadden reached a settlement with the Justice Department. But prosecutors in Washington are weighing charges against Skadden’s lead lawyer on the firm’s work in consultation with Mr. Manafort in 2012 on behalf of the Ukrainian government, while the Southern District has retained control of the investigations of Mercury and the Podesta Group, according to people familiar with the matter.
The Southern District’s reputation for nonpartisanship — and history of autonomy from the Justice Department in Washington, giving it the nickname “Sovereign District” — may make it less vulnerable to attacks from the president and his allies. The president’s lead lawyer, Rudolph W. Giuliani, led the office from 1983 to 1989 and later became New York’s mayor.
The Southern District’s role in Trump-related cases comes at a time of transition for the office, which is led by Geoffrey S. Berman, who was appointed in January 2018 by the Trump administration.
Mr. Berman notified Justice Department officials early last year of a possible appearance of a conflict of interest in the Cohen investigation, and officials concluded that he should be recused, for reasons that have not been disclosed.
In his stead, Mr. Berman’s handpicked deputy, Robert S. Khuzami, led the Cohen investigation. But on Friday, Mr. Berman announced that Mr. Khuzami will step down from his post next month to return home to Washington.
Mr. Berman named his senior counsel, Audrey Strauss, as Mr. Khuzami’s successor. Ms. Strauss, who had already been deeply involved in the Cohen investigation, will assume responsibility for any remaining aspects of the Cohen inquiry that were subject to Mr. Berman’s recusal.
Mr. Khuzami’s departure will not directly affect most of the other Trump-related investigations, which Mr. Berman has supervised. Mr. Berman’s name, for example, appeared on a February grand jury subpoena served on the president’s inaugural committee.
For the most part, the investigations surrounding the president and his associates have been assigned to career prosecutors in the office’s public corruption unit, which has a track record of convicting politicians on both sides of the aisle. Those prosecutors work on the eighth floor of the building, down the hall from Mr. Berman’s office.
The unit is led by two office veterans, Russell Capone and Edward B. Diskant, and although line prosecutors shift in and out — one assistant who worked on the Cohen inquiry, Rachel Maimin, recently went into private practice, and another, Andrea M. Griswold, returned to work full time on securities cases — the unit has a deep bench.
Two prosecutors who worked on the Cohen case, Thomas McKay and Nicolas Roos, remain in the unit. The investigations are overseen by the office’s criminal division, which recently got a new chief, Laura G. Birger; she succeeded Lisa Zornberg, who left the office to return to private practice.
Robert B. Fiske Jr., a former United States attorney in Manhattan who later served as the first independent counsel investigating the Whitewater matter during the Clinton administration, said the Southern District prosecutors would maintain the kind of professionalism associated with Mr. Mueller’s team.
“If the question is, should the public have confidence that there will be the same kind of integrity and independence in the Southern District of New York that there has been in the Mueller investigation, the answer is absolutely,” Mr. Fiske said.