President Trump fired FBI Director James B. Comey, who was fewer than four years into what was supposed to be a 10-year term, on Tuesday evening. His ouster, which purportedly came because he mishandled the investigation of then-Secretary of State Hillary Clinton’s private email server, is just the the second firing of an FBI director in history — the other by President Bill Clinton for ethical violations.

The firing comes as the FBI is investigating the Trump campaign’s ties to Russian officials. The dismissal now allows Trump to replace Comey, who was appointed by Obama but has served under presidents of both parties, with his own appointee.

That potential conflict of interest — an ally of the president, whether a Trump appointee or another member of his party, controlling the agency that is investigating Trump — is echoed across the different agencies and committees with a hand in the investigation.

That doesn’t mean, of course, that those individuals are actually shirking their responsibilities — just that they don’t appear to be an unbiased third party.

The intelligence agencies’ directors will be Trump appointees

The FBI, which will eventually be run by a Trump appointee, has the largest role in intelligence gathering regarding the Trump-Russia inquiry and broader authority to investigate U.S. citizens than the other intelligence agencies. The agency’s findings go to higher-ups in the Justice Department, and some information also goes to Congress.

The FBI director has significant power to determine how thorough the investigation will be. He or she can decide on the size and scope of the investigation. The director can also refuse to cooperate with congressional inquiries, among other things.





Other intelligence agencies also have a role in this intelligence gathering, though they focus more on foreign agents. The Director of National Intelligence oversees a large swath of intelligence officials, most notably the CIA and NSA directors. All of these officials do not report their findings to the Justice Department but do relay information to Congress, either at their discretion or in response to subpoenas.

Much like in the case of the FBI, these directors have discretion to put fewer resources toward the investigation or minimize cooperation with Congress.





The Justice Department leaders are Trump appointees

Based on the evidence turned up by the FBI’s investigation, the Justice Department is able to file and prosecute criminal charges. The person leading that investigation has significant discretion over what those charges are, so they could minimize the consequences any wrongdoers face. Though, if the evidence was stark, there would be a lot of political pressure to file significant charges.





Trump’s party controls Congress

The House and Senate’s investigations have a broader scope than the DOJ’s and can look into actions that are problematic or unethical, not just illegal. They can respond to wrongdoing by making the results of their investigation public and creating political pressure for the official in question to be dismissed. Though it’s rarely done, especially to officials of the same party, they could also impeach officials.

Congressional Republicans have a clear stake in minimizing the reach of the Trump-Russia investigation. If the investigation’s results cast Trump in a negative light, it would reflect poorly on the party as a whole, making it harder to pass legislation or get reelected. Since Republicans control both houses of Congress, the scope and content of the investigation is completely up to their members leading the intelligence committees. So, it’s easy to tone the investigation down if there’s not too much political pressure.

That doesn’t mean they will — the intelligence committees have a long history of bipartisan cooperation. Many Republican lawmakers have expressed serious concern about Russia’s alleged interference in the presidential election and how Trump has responded to it. Sen. Richard Burr (R-N.C.), for instance, who’s running the Senate’s investigation, said he was “troubled by the timing and reasoning of Director Comey’s termination.”





Citing these conflicts of interest throughout the system, lawmakers (primarily but not exclusively Democrats) have called for a special prosecutor or independent commission to take control of the Russia investigation.

Such a move would increase the independence of the investigation, but it may not be enough. The independent party may rely in part on intelligence collected by the FBI or other agencies — organizations that, after Comey’s dismissal, will soon all be overseen by Trump’s allies.