Paul Manafort’s legal team is trying to show that his longtime Ukraine employee was a U.S. asset and not necessarily a Russian spy, as portrayed by special counsel Robert Mueller, a court filing shows.

Constantin Kilimnik, the man pegged by the Mueller team and the press as a spy, communicated with the U.S. Embassy in Kiev during Ukraine’s political upheaval, a hearing transcript shows.

Not mentioned in the filing is the fact that Mr. Kilimnik also worked in the 2000s in Moscow for the Washington-based International Republican Institute, a pro-democracy nonprofit led by Sen. John McCain for 25 years.

A censored transcript of a Feb. 4 closed hearing shows Mueller top gun Andrew Weissmann is still pursuing Trump-Russia collusion.

No Trump person has been charged with conspiracy well into the investigation. Mr. Kilimnik appears to be Mr. Weissmann’s key.

The presence of Mr. Kilimnik, a Ukraine-born Russian citizen, keeps alive the theory that Manafort, President Trump’s former campaign manager, conspired with Moscow during the 2016 election.

The suspicion heated up Wednesday, when U.S. District Judge Amy Berman Jackson ruled that Manafort lied to prosecutors during his cooperation phase about meetings he had with Mr. Kilimnik.

Defense attorney Kevin Downing blamed any inconsistencies on a faulty memory. “Mr. Manafort did not lie,” he said in a Wednesday filing.

Manafort has been convicted of bank and tax fraud. He has not been charged by Mr. Mueller of any conspiracy with Russian election interference; neither has Mr. Kilimnik.

The redacted transcript of the hearing before Judge Jackson showed that Mr. Downing has pressed the Mueller team to turn over any evidence of Mr. Kilimnik working with the U.S. Embassy in Kiev. He made the request under the so-called Brady rule, which resulted from a 1963 U.S. Supreme Court decision that requires prosecutors to provide the defense with evidence that is exculpatory for the defendant.

The hearing centered on Mr. Mueller’s assertion that Manafort violated his plea deal by lying about his contacts with Mr. Kilimnik at an Aug. 2, 2016, session at New York City’s Grand Havana Room cigar bar, and at several post-election meetings.

Mr. Weissmann told the judge he met the Brady request by talking to the State Department and confirming that Mr. Kilimnik in fact did have contacts the U.S. Embassy.

Here is how Mr. Weissmann described the Brady material: “The defense as is their right asked us early on in the case to produce any and all communicants with the American embassy in Ukraine. And so we then went to the State Department to get communications that were either direct or indirect by Mr. Manafort with the State Department. So Mr. Kilimnik was encompassed in that search. There is no question that Mr. Manafort had communications with people at the State Department. There’s no question that Mr. Kilimnik did.”

The transcript’s next block of comments are blacked out. Then Mr. Weissmann said: “There are definitely communications that Mr. Kilimnik has with people in the State Department. I don’t see how that is in any way relevant to this issue before the court.”

Mr. Weissmann said Mr. Kilimnik “is understood by the FBI, assessed to be — have a relationship with Russian intelligence.” The prosecution hasn’t produced evidence of that supposed relationship in open court.

The Washington Times asked the State Department what role, if any, Mr. Kilimnik played for the embassy in Kiev.

“As a general matter, embassies meet with a wide range of people. To the extent you have questions about testimony in the Manafort case, we refer you to the Office of Special Counsel,” a spokesperson said.

Why is it important now that Manafort stands convicted and is awaiting sentencing?

Because Mr. Mueller is still investigating the August 2016 meeting when Manafort served as campaign manager. In attendance were Mr. Kilimnik and Rick Gates, a former Manafort business partner who turned state’s evidence. The censored transcript suggests Gates privately has made new charges about that meeting.

Mr. Weissmann apparently is trying to show that the two discussed sanctions relief for Russia should Donald Trump become president.

“This goes, I think, very much to the heart of what the special counsel’s office is investigating,” Mr. Weissmann told the judge.

A legal expert not involved in the case told The Times that it is clear the defense is trying to undercut the Russian intelligence-link allegation by collecting evidence that Mr. Kilimnik was a U.S. asset.

“If the U.S. trusted Kilimnik, then they must not think he’s a Russian spy,” the legal expert said. “This blows another hole in the entire Russian collusion theory.”

Mr. Downing told the judge that Mr. Weissmann’s collusion theory “is nonsense because no matter who gets elected, that the sanctions were going to continue against Russia I think you need to consider this rank speculation.”

Mr. Mueller brought two obstruction of justice charges against Mr. Kilimnik for allegedly conspiring with Manafort to tamper with a witness. The issue was not election collusion, but how Manafort failed to register with the Justice Department as a lobbyist for the pro-Russia Party of Regions in Ukraine.

During the Mueller probe, Mr. Kilimnik was interviewed by the FBI. He has not appeared in court to face charges. Court filings say that, after his indictment, he feared for his safety in Ukraine and moved to Russia.

After being convicted of bank fraud in a Virginia court, Manafort appeared before Judge Jackson to plead guilty to witness tampering and other charges. Her order on Wednesday nullified his plea deal, meaning the prosecution is no longer bound to recommend a lenient sentence next month.

Mr. Kilimnik served in the Russian military and did translations for intelligence units. He has denied he worked for Russian intelligence post-military, including the time he was Manafort’s officer manager and translator in Ukraine.

A longtime Republican operative, Manafort collected millions of dollars in consulting fees from the Party of Regions, Ukraine’s largest. He hid the income from the U.S. to avoid taxes.

Before joining Manafort’s firm, Mr. Kilimnik had another connection to the West: He worked to promote democracy as a translator and on other assignments for the International Republican Institute.

Responding to a query, an IRI spokesperson provided this statement to The Times: “Konstantin Kilimnik worked in IRI’s Moscow office from 1995 until 2005. He started out as a translator but took on a number of other tasks. He hasn’t worked for IRI in 13 years, nor have we had any relationship with him. Kilimnik was fired from IRI’s Moscow office as soon as the Institute became aware that he was joining Paul Manafort’s team to work on their Ukraine account.”

When he resigned as IRI chairman shortly before his death from brain cancer, the late McCain praised IRI workers.

“In my years as chairman, I have been privileged to watch generations of young IRI foot soldiers serve a cause greater than their self-interest,” he said.