The mood at the F.B.I. is dark, and nobody is willing to predict what the coming days will bring, particularly if agents and analysts do not complete their review of Ms. Abedin’s emails by Election Day. Officials said it would take something extraordinary to change the conclusion that nobody should be charged. But the absence of information has allowed festering speculation that the emails must be significant.
Daniel C. Richman, an adviser to Mr. Comey and a Columbia University law professor, argued that despite the backlash, Mr. Comey’s decision to inform Congress preserved the F.B.I.’s independence, which will ultimately benefit the next president.
“Those arguing that the director should have remained silent until the new emails could be reviewed — even if that process lasted, or was delayed, until after the election — give too little thought to the governing that needs to happen after November,” Mr. Richman said. “If the F.B.I. director doesn’t have the credibility to keep Congress from interfering in the bureau’s work and to assure Congress that a matter has been or is being looked into, the new administration will pay a high price.”
Former senior law enforcement officials in both parties, though, say Mr. Comey’s decision to break with Justice Department guidelines caused these problems. Had he handled the case the way the F.B.I. handled its investigations into the Clinton Foundation and Mr. Manafort over the summer, the argument goes, he would have endured criticism from Republicans in the future but would have preserved a larger principle that has guided cases involving both parties.
In the Ukraine case, agents in Washington are investigating the relationship between foreigners and Mr. Manafort, who was Mr. Trump’s campaign chairman from June until August. For a decade beginning in 2005, Mr. Manafort advised Ukrainian politicians, including Viktor F. Yanukovych, who served as president from 2010 to 2014, when he fled the country amid protests.
The cases involving Mr. Manafort and Mrs. Clinton were described by federal law enforcement officials who spoke on the condition of anonymity because they were not authorized to discuss open investigations.
In an email, Mr. Manafort denied the existence of an F.B.I. investigation into his business dealings and said that reports of one were “an outrageous smear being driven by” Democrats who are trying to distract attention from Ms. Abedin’s emails. “There is nothing of my business activities to investigate,” he said.
In August, The New York Times reported that anti-corruption investigators in Ukraine had found handwritten ledgers showing $12.7 million in undisclosed payments to Mr. Manafort. The investigators, from Ukraine’s newly formed National Anti-Corruption Bureau, assert that the payments were part of an illegal off-the-books system whose beneficiaries also included elected officials.
The Times reported that other prosecutors in Ukraine were examining a group of offshore shell companies that members of Mr. Yanukovych’s inner circle had used to fund lavish lifestyles, including a presidential residence with a private zoo, golf course and tennis court. Those prosecutors are looking at many transactions that involved Mr. Manafort, including an $18 million deal that sold Ukrainian cable television assets to a partnership put together by Mr. Manafort and a Russian oligarch, Oleg Deripaska, a close ally of President Vladimir V. Putin of Russia.
Four days after The Times published the story about Mr. Manafort’s business dealings, he resigned as Mr. Trump’s campaign chairman. The F.B.I.’s criminal investigation continues, though agents have followed the Justice Department’s guidance and have not taken overt steps in the case.
In August, around the same time the decision was made to keep the Manafort investigation at a low simmer, the F.B.I. grappled with whether to issue subpoenas in the Clinton Foundation case, which, like the Manafort matter, was in its preliminary stages. The investigation, based in New York, had not developed much evidence and was based mostly on information that had surfaced in news stories and the book “Clinton Cash,” according to several law enforcement officials briefed on the case.
The book asserted that foreign entities gave money to former President Bill Clinton and the Clinton Foundation, and in return received favors from the State Department when Mrs. Clinton was secretary of state. Mrs. Clinton has adamantly denied those claims.
In meetings, the Justice Department and senior F.B.I. officials agreed that making the Clinton Foundation investigation public could influence the presidential race and suggest they were favoring Mr. Trump. But waiting, they acknowledged, could open them up to criticism from Republicans, who were demanding an investigation.
They agreed to keep the case open but wait until after the election to determine their next steps. The move infuriated some agents, who thought that the F.B.I.’s leaders were reining them in because of politics.
Mr. Comey’s allies say he could not have simply followed this script last week when he learned that agents had discovered new emails on a laptop belonging to Ms. Abedin’s estranged husband, Anthony D. Weiner. News of the search would surely leak, he concluded, and it would appear that he had withheld the information from Congress. He also thought that he alone was a trusted voice on the Clinton case because of Attorney General Loretta E. Lynch’s highly criticized meeting with Mr. Clinton in the original investigation’s final days, officials said.
But F.B.I. agents, many of whom are strongly supportive of Mr. Comey and his approachable leadership style, have struggled to defend his decision. They acknowledge that he was in a bind, but say the backlash against the F.B.I. is unlike any in recent history.
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