Washington — The mystery at the center of the Michael Flynn case is why Donald Trump didn’t react sooner to warnings about Flynn’s involvement with Russia. Why didn’t Trump listen to President 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”?

We don’t have answers. But one obvious possibility is that President Trump didn’t take action because he already knew about Flynn’s Dec. 29 discussion with Ambassador Sergey Kislyak about sanctions, and knew that Flynn had misrepresented the Kislyak call to Vice President Mike Pence.

Flynn’s discussion with the Russian ambassador at such a sensitive time, when the U.S. 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 this 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 the 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 the Flynn case, Trump delayed removing him, claimed Flynn had done nothing wrong even as he fired him, and said he should be given immunity. Meanwhile, Trump fired Yates at Justice (for refusing to carry out his immigration ban) and later shot off a tweet needling her the morning she appeared before the Senate committee.

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 traits 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,” “candidly” or “truthfully.” The authors’ point is that people who are innocent answer questions simply and directly, rather than embellishing their answers with phrases like “to tell you the truth,” or “I swear to God.”

As the authors pointedly note: “Truth fears no questions.” They quote an unforgettable comment by Thomas Jefferson in a 1785 letter to a nephew: “He who permits himself to tell a lie once finds it much easier to do it a second or third time, till at length it becomes habitual.”

Yates offered a vivid account of why Justice Department officials were concerned about Flynn’s conduct and the lack of a White House response. They feared that Russian intelligence had secret leverage over the person entrusted with the nation’s most sensitive secrets. Even after Yates’ initial explanation on Jan. 26, White House Counsel Donald McGahn didn’t seem to get it. “Why does it matter to DOJ if one White House official lies to another White House official?” Yates says he asked the next day.

“So we explained to him,” Yates continued, “the concern first about the underlying conduct itself, [and] that he had lied to the vice president and others. The American public had been misled. And then importantly, that every time this lie was repeated … it increased the compromise. And to state the obvious, you don’t want your national security adviser compromised with the Russians.”

The Russia investigation isn’t the only issue that matters to the country, or even necessarily the most important one. But it’s a criminal probe of a significant counterintelligence case. If the FBI and Justice Department weren’t trying to get answers about whether Russia’s covert actions had any connection with the Trump campaign, it would be a gross breach of their responsibility.

Sen. Sheldon Whitehouse, the Rhode Island Democrat who co-chaired Monday’s hearing, summed up the Trump puzzle for me this way: “President Trump called Flynn ‘a fine person’ who was ‘just doing his job.’ This might simply be evidence of an ill-prepared White House in disarray, but that doesn’t explain the president’s dogged protection of Flynn. There’s something going on here, and Congress needs to find out what it is.”

— David Ignatius is a columnist for Washington Post Writers Group.