President Trump’s abrupt firing of FBI Director James B. Comey will intensify focus on the issue Trump has been so eager to dismiss — his knowledge of contacts between Michael Flynn and other associates and Russia.

White House arguments that Trump sacked Comey for mishandling the investigation of Hillary Clinton’s emails are implausible, but no more so than some of the arguments the Trump team has made about Flynn’s firing in February. Sources say the White House has been talking about firing Comey since before the inauguration; why they pulled the trigger now is unclear, but FBI agents, including those who dislike Comey, were said to be dazed and upset Tuesday night.

The Comey putsch heightens the mystery at the center of the Flynn case: Why Trump didn’t react sooner to warnings about Flynn’s involvement with Russia. Why didn’t Trump listen to President Barack Obama’s caution against hiring him? Why did Trump wait 18 days before removing his national security adviser after urgent advice that Flynn could be “blackmailed”?

After Comey’s dismissal, critics are likely to examine more sharp-edged theories of the Flynn case and other Russia matters. One obvious possibility is that Trump didn’t take action earlier because he already knew about Flynn’s Dec. 29 discussion with Russian Ambassador Sergey Kislyak about sanctions, and knew that Flynn had misrepresented the Kislyak call to Vice President-elect Mike Pence.

Flynn’s discussion with the Russian ambassador at such a sensitive time, when the United States was punishing Russia for hacking the 2016 election, was arguably a violation of the Logan Act, which bars private meddling during a confrontation with another country. It was “problematic” behavior, as former acting attorney general Sally Yates said in her riveting testimony Monday.

But the Kislyak call wasn’t a hanging offense, and it probably wasn’t even a prosecutable one. Trump could have said back on Dec. 29 that Flynn had talked with Kislyak in hopes of averting Russian reprisals for U.S. sanctions announced that day. Trump certainly wasn’t shy about crediting President Vladimir Putin on Dec. 30 for his “great move” in not retaliating. Is it really plausible that Trump hadn’t talked to Flynn before posting that tweet?

Trump has been digging a hole for himself from the beginning on Russia-related issues. It’s an odd pattern of behavior. Trump may have done nothing improper involving Russia, but why does he act so defensive?

In a book called “Spy the Lie,” a group of former intelligence officers explain the behavioral and linguistic cues that indicate when someone is being deceptive. Interestingly, many of these are evident in Trump’s responses to questions about Russia’s covert involvement in U.S. politics.

The authors’ list of tip-offs includes “going into attack mode,” “inappropriate questions,” “inconsistent statements,” “selective memory” and the use of “qualifiers,” such as “frankly,” “honestly” and “truthfully.” The authors’ point is that people who are innocent answer questions simply and directly.

Comey’s firing takes the country closer to the dangerous collision that has been looming since allegations began about possible connections between Trump and his associates and the Russian covert influence operation Comey has been investigating since July.

Trump will now appoint a new FBI director whose mission will include investigating Trump himself. Attorney General Jeff Sessions, having recused himself from the Russia investigation, will now face criticism that he reneged on his promise by recommending the firing of the person leading the probe.

The most delicate role in this dark tale is the one played by Deputy Attorney General Rod J. Rosenstein. He has been widely praised as a solid prosecutor. But his long, rambling letter supporting Comey’s removal was closer to a civics essay than a lawyerly statement. It cited a grab bag of op-eds and public statements to scold Comey.

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For a newcomer to a top role at the Justice Department, Rosenstein was strangely insistent: “The FBI is unlikely to regain public and congressional trust until it has a Director who understands the gravity of the mistakes and pledges never to repeat them. Having refused to admit his errors, [Comey] cannot be expected to implement the necessary corrective actions.”

Will the next FBI director truly be free to pursue the investigation that Comey began? Will a bureau already riven by political divisions and back-biting truly regain confidence and public trust? Can the Justice Department oversee the Russia matter? Already, congressional pressure is building for an independent counsel — which is the most sensible way to restore a measure of public confidence after this debacle.

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