The FBI under James B. Comey “unilaterally” made the decision to interview retired Lt. Gen. Michael Flynn, excluding input from the Justice Department, ignoring the White House counsel and leading Flynn to believe agents were arriving as friends to discuss terrorism, his lawyer says.

Mr. Comey, after being fired by President Trump, later bragged in public that he sent Peter Strzok and another agent to the White House on Jan. 24, 2017, knowing he could capitalize on a chaotic place.

Sidney Powell, Flynn’s attorney, told District Judge Emmet Sullivan in a new court filing that FBI higher-ups strategized the day before for what she called an “ambush.”

“When the Director of the FBI, and a group of his close associates, plot to set up an innocent man and create a crime — while taking affirmative steps to ensnare him by refusing to follow procedures designed to prevent such inadvertent missteps — this amounts to conduct so shocking to the conscience and so inimical to our system of justice that it requires the dismissal of the charges for outrageous government conduct,” Ms. Powell wrote.

Then-Deputy FBI Director Andrew McCabe, who would later be fired for allegedly lying about an unrelated leaked news story, telephoned Flynn the day before to arrange a no-lawyer interview.

Mr. Strzok found Flynn “relaxed and jocular” and “unguarded.”

“This and Strzok’s admissions make clear that Comey and McCabe were executing their own agenda — not investigating a crime,” Ms. Powell said.

Flynn pleaded guilty in December 2017 to lying to the agents when he said he didn’t discuss Obama-imposed sanctions with Russian Ambassador Sergey Kislyak when they spoke during the transition. In fact, a transcript in the agents’ possession showed he did.

He became a cooperating witness in the Russian election interference probe by special counsel Robert Mueller. Flynn had no information on any conspiracy, which Mr. Mueller said in March he didn’t find.

Ms. Powell is accusing the Mueller team of withholding favorable evidence, called “Brady,” as ordered by the judge. Flynn did not know until the day after he pleaded guilty the degree to which Mr. Strzok despised President Trump as expressed in text messages.

Ms. Powell’s latest brief is a response to a reply from Special Assistant U.S. Attorney Brandon L. Van Grack. He called Ms. Powell’s previous assertions “conspiracy theories.” He said that all of her requested documents either didn’t exist or were immaterial.

After leaving the White House that day, Mr. Strzok texted FBI counsel Lisa Page, then his lover.

Mr. Strzok texted Page: “Describe the feeling, nervousness, excitement knowing we had just heard him denying it all. Knowing we’d have to pivot into asking. Puzzle round and round about it. Talk about the funny details. Remember what I said that made Andy [McCabe] laugh and ask if he really said that.”

Ms. Powell wrote, “In this case, high-ranking FBI officials orchestrated an ambush-interview of the new president’s National Security Advisor, not for the purpose of discovering any evidence of criminal activity — they already had tapes of all the relevant conversations about which they questioned Mr. Flynn — but for the purpose of trapping him into making statements they could allege as false.

Ms. Powell said that the FBI’s report on the Flynn interview, called a 302, was changed to make him look guilty. Mr. Flynn had said he was not sure he spoke to Mr. Kislyak about a United Nations vote. The FBI, after news of the conversation leaked to The Washington Post, changed the 302 to “Flynn stated he did not.”

“This is deceptive manipulation,” Ms. Powell said.

“The government continues to hide evidence of the original 302, other exculpatory texts, and other forms of information completely,” Ms. Powell said.

On May 9, 2017, the day after Mr. Comey was fired, Mr. Strzok texted: “We need to open the case we’ve been waiting on now while Andy is acting.”

The next day, he opened an obstruction of justice case against Mr. Trump, as well as a counterintelligence probe to see if he was a Russian agent.

In the background, as the FBI tried to nail Flynn, was the Democratic Party-financed dossier circulated in the bureau by Hillary Clinton operatives. It alleged falsely that Trump aides were in an extensive conspiracy with Moscow.

Ms. Powell accused prosecutor Van Grack, a veteran of the Mueller team, of providing false information when he said only one 302 version existed.

She said, “The evidence the defense requests, if produced, would defeat the factual basis for the plea. The original 302 is crucial to this as are the original notes. The government elides the truth that the FBI has it and any other drafts prior to February 10, 2017.”

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