Then-Deputy Attorney General Rod Rosenstein was determined to keep his big secret about a pending special counsel right up to the day his top candidate, Robert Mueller, sat down with President Trump in the Oval Office.

“The boss and his staff do not know about our discussions,” Mr. Rosenstein said in an email to Mr. Mueller on May 12, 2017.

Mr. Rosenstein’s “boss” was an apparent reference to Attorney General Jeff Sessions, who had stepped away from any role in the Russia probe. This meant that Mr. Trump didn’t know, either.

The email was one of a thread of messages that the conservative watchdog group Judicial Watch obtained from the Justice Department under a Freedom of Information Act lawsuit.

Mr. Trump has claimed that the purpose of Mr. Mueller’s May 16 White House visit was to interview him for the vacant FBI director post. Mr. Mueller, a former FBI director, has said the meeting’s purpose was to discuss the bureau in general.

Whatever the purpose, John Dowd, Mr. Trump’s attorney during the ensuing 22-month probe, said Mr. Mueller had a duty not to meet with the president knowing he was likely to be investigating the Trump campaign.

“The most dishonorable conduct I have ever witnessed,” Mr. Dowd told The Washington Times.

Noting Mr. Mueller’s military service, Mr. Dowd added: “Capt. Robert Mueller, USMC, sits in front of his commander-in-chief being interviewed for FBI director knowing he is going to investigate the president and never says a word.”

That same day, May 16, Mr. Mueller also visited Mr. Rosenstein at the Justice Department.

“I am with Mueller,” Mr. Rosenstein said in an email to Mark Filip, a former deputy attorney general now in private law practice. “He shares my view. Duty calls. Sometimes the moment chooses us.”

The next day, Mr. Rosenstein shocked the White House. Without consultation, he announced that Mr. Mueller would take over the Russia probe, launching a historic investigation that would attract a staff of mostly Democratic prosecutors. He gave Mr. Mueller wide latitude to investigate Mr. Trump and his campaign associates, saying “any links” with Russia should be probed.

May 2017 was a particularly tumultuous month inside the Justice Department and the FBI.

Mr. Trump fired FBI Director James B. Comey on May 9. The White House cited a memo written by Mr. Rosenstein on how Mr. Comey crossed the line in announcing no charges against Hillary Clinton for her mishandling of State Department emails.

Aghast, Mr. Rosenstein almost immediately began a hunt for a special counsel. His inbox filled with demands from liberal nonprofit groups to appoint one. He didn’t believe he had written the memo to justify a firing.

The next day, Mr. Rosenstein made his first overture to Mr. Mueller.

An aide emailed Mr. Mueller’s law firm, WilmerHale: “I’m writing to try to arrange a meeting between Mr. Rosenstein and Bob Mueller, hopefully for Friday [May 12] morning — anytime before 10 a.m. Can you let me know if Mr. Mueller would have any time? Thanks so much!”

A Mueller assistant replied 24 minutes later: “Can we do it at 8 a.m.? Also would it be possible to get a parking spot for Mr. Mueller inside the building.”

On the night of May 12, Mr. Rosenstein sent the boss-doesn’t-know email to Mr. Mueller.

The next morning, Mr. Mueller wrote to Mr. Rosenstein: “Rod if you have a moment would you please give me a call.”

By May 16, the deal seemed done. Mr. Rosenstein again met with Mr. Mueller and sent the “sometimes the moment chooses us” email. Mr. Mueller spent time that same day with the president. Mr. Rosenstein announced the appointment on May 17.

“These astonishing emails further confirm the corruption behind Rosenstein’s appointment of Robert Mueller,” said Judicial Watch chief Tom Fitton.

Judicial Watch released documents in September about another traumatic event unfolding inside the Justice Department that May.

Mr. Rosenstein, acting FBI Director Andrew McCabe and other aides met to discuss the Comey firing — the same day Mr. Rosenstein met with Mr. Mueller and Mr. Mueller met with Mr. Trump.

The group’s suspicions immediately turned on Mr. Trump as a target in the Justice Department’s Russia election interference probe.

In an astounding discussion, Mr. Rosenstein offered to wear a wire during a meeting with the president to record the conversation and ask him his motivations, according to a contemporaneous memo written by Mr. McCabe.

“He said he thought this might be possible because he was not searched when he entered the White House,” Mr. McCabe wrote. “I told him that I would discuss the opportunity with my investigative team and get back to him.”

The wire caper apparently never happened.

Mr. McCabe, who would be fired the next year for allegedly lying to investigators about a leaked news story, acted on May 16 to investigate Mr. Trump as a possible Russian spy and election collaborator.

A year later, Mr. Rosenstein discussed how to respond to a 2018 New York Times story about the wire and about invoking the 25th Amendment to remove an incapacitated president.

The story apparently came from the fired Mr. McCabe. He talked about the incident while selling his book, “The Threat.”

Mr. Rosenstein ended up issuing a statement: “The New York Times’s story is inaccurate and factually incorrect. I will not further comment on a story based on anonymous sources who are obviously biased against the Department and are advancing their own personal agenda. But let me be clear about this: Based on my personal dealings with the President, there is no basis to invoke the 25th Amendment.”

Mr. Mueller completed his final report in March. While Mr. McCabe implied that Mr. Trump is a Russian spy, the 448-page report offers no such evidence. Mr. Mueller was assigned to find “any links” with Russia by any Trump associate or Mr. Trump himself.

The Mueller report said: “The evidence we obtained did not establish that the president was involved in an underlying crime related to Russian election interference.”

In July, Mr. Mueller appeared before two House committees at the insistence of Democrats.

Rep. Louie Gohmert, Texas Republican, asked him about his May 16, 2017, meeting with the president.

Asked whether he planned to investigate Mr. Trump for firing Mr. Comey at the time he was appointed special counsel, Mr. Mueller answered, “I’m not going to get into that. Internal deliberation from the Justice Department.”

“Were you talking to him about FBI director position,” Mr. Gohmert asked.

“Not as a candidate,” Mr. Mueller said.

“Did he mention the firing of James Comey in your discussion with him?” the congressman asked.

“Cannot remember,” Mr. Mueller said. “I don’t believe so, but I’m not going to be specific.”

“If he did, you could have been a fact witness as to the president’s comments and state of mind on firing James Comey,” Mr. Gohmert said.

“I suppose that’s possible,” Mr. Mueller said.

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