The FBI director has faced loud criticism over his handling of the Clinton email investigation. Regardless of who wins the election, he is poised to pay a price

Hillary Clinton’s immediate FBI woes ended on Sunday with a letter whose five sentences signaled that James Comey’s troubles have only begun.

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The director of the FBI has come under withering, escalating and relentless criticism since he sent Congress a vague letter, on 28 October, heralding a potential re-examination of the investigation into Clinton’s private email server. The original inquiry ended in July, after months of officials scouring Clinton’s communications while secretary of state, with the conclusion that her practices were “extremely careless” but not criminal.

On Sunday, Comey brought what many viewed as a frightening FBI intervention into a presidential election to a close. The Democratic presidential nominee will not face an FBI recommendation for indictment over her stewardship of classified information.

Whether or not Comey endangered his position at the head of the FBI, the episode has cost him his chief asset: his reputation, cultivated assiduously in the media, for probity and judgment. Beyond the director himself, the coda to the Clinton email inquiry has exposed the FBI as a politicized agency, a development with serious repercussions over the next several years.

Donald Trump spent much of the summer and fall attacking the FBI as “corrupt” for failing to recommend indictment, only to reverse himself entirely after Comey’s October letter. Now that Comey has ended the issue ahead of the election, the director has demonstrated himself to be an unreliable ally to Trump, who has loudly insisted on complete loyalty around him. Should Trump win the election, Comey is likely to find himself either marginalized or unemployed.

If Clinton wins, Comey’s position is unlikely to be much better.

Sources within the FBI have pointed to a deep, visceral antipathy to Clinton within the bureau, as well as substantial support for Trump. Comey’s earlier decision to publicly recommend no charges had spurred anger among FBI employees disposed negatively toward her, and Comey’s newest letter changes none of that sentiment. Now Comey has restored that status quo ante, again frustrating anti-Clinton sentiments in his workforce. This time, however, he has seen his allies in Washington abandon him, depriving Comey of a bulwark against his rank-and-file.

The loss of that bulwark is critical, and will likely become visible in the near future. Beyond the email inquiry, the FBI also has had the Clinton Foundation, the family’s charity, under some form of scrutiny.

Once again, Comey is in a bind. FBI sources have already leaked that allegations against the foundation are weak, given their source in a book by a far-right author who provides little evidence. Should the FBI fail to recommend another indictment, Trump’s voters and congressional Republicans will presume bias in the bureau – particularly since those Republicans have already stated intentions to keep a hypothetical Clinton White House under persistent investigation. Should the FBI recommend indictment, Clinton’s voters and congressional Democrats will presume Comey acted for political reasons, or caved to such motives within the bureau.

Comey may very soon himself be under investigation. Al Franken, a Minnesota senator on the judiciary committee with direct oversight of the FBI, said early Sunday he was “certain” of forthcoming hearings into Comey’s actions. After the latest letter, Senator Dianne Feinstein, another judiciary committee Democrat and a consistent ally of the security agencies, said she found Comey’s intervention “even more troubling”. Feinstein also called for a justice department review.

Clinton herself has pointedly declined to say whether she would retain Comey if she is elected. She too faces a political dilemma, even in the event of victory on Tuesday, since firing Comey could turn the director into a martyr for opponents on the right. Clinton’s chief aides are notorious for their long memories, however, and her White House would likely view the FBI as a threat, or at least with extreme distrust. Her appointment of an attorney general would consequently fall under intense questioning about any tacit mandate to contain the bureau.

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Comey’s political imbroglio coincides with his attempt to persuade Congress that sophisticated commercial encryption poses a security threat. He has now lost his chief weapon in that debate, the benefit of the doubt: FBI intervention into a presidential election has made fears of an assertive law enforcement and intelligence agency deciding the national agenda more salient than any PR campaign from privacy advocates ever could.

It is a spectacular fall for Comey. He built his public persona as the man who stood up to pressure from George W Bush’s White House over mass surveillance. The real story, hidden from public view until Edward Snowden’s leaks, showed Comey to be significantly less heroic, but the persona was enough to persuade Barack Obama to elevate him to run the FBI weeks after the Guardian began publishing material Snowden disclosed. After Comey picked a fight with Apple over encryption and lost, his judgment appeared shaky.

Now Comey has committed an unforced error that has drained his reservoir of goodwill in Washington. With the FBI’s integrity in the balance, Comey faces several difficult months, if not years, in Washington, regardless of the country’s vote in two days.