WASHINGTON (Reuters) - A federal judge tore into all of the legal arguments that a lawyer for President Donald Trump’s former campaign chairman Paul Manafort made on Wednesday in his long-shot civil case to convince her that Special Counsel Robert Mueller’s investigation has run amok and should be reined in.

“I don’t really understand what is left of your case,” U.S. District Court Judge Amy Berman Jackson said to Kevin Downing, Manafort’s attorney, after peppering him with a lengthy series of questions.

Manafort filed a civil lawsuit on Jan. 3 in the U.S. District Court for the District of Columbia against Mueller and Deputy Attorney General Rod Rosenstein, the Justice Department official who appointed the special counsel, in a key legal test of how far Mueller’s mandate extends.

Jackson did not say when she might rule on the civil case, which the Justice Department is seeking to dismiss.

Mueller is investigating possible collusion between Trump’s campaign and Russia as well as whether the president has unlawfully tried to obstruct the probe.

Mueller has charged 22 individuals and entities to date, including Manafort and his associate Rick Gates. Manafort’s civil case marks the first time a defendant has sought to challenge his authority.

Manafort, who performed lobbying work for a pro-Russian former Ukrainian president before serving as Trump’s campaign chairman in 2016, is facing two indictments brought by Mueller in federal courts in Washington and Alexandria, Virginia. The charges against him include conspiring to launder money, failing to register as a foreign agent, bank fraud and filing false tax returns.

Manafort has pleaded not guilty and none of the charges directly relate to work he performed for Trump’s campaign.

Trump has denied colluding with Russia and called Mueller’s probe a witch hunt.

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Manafort’s civil lawsuit relies on an arcane law called the Administrative Procedure Act, which spells out the process federal agencies must follow when writing regulations. The suit alleges that Rosenstein’s order laying out Mueller’s investigative mandate violates Justice Department rules because it is overly broad and therefore “arbitrary and capricious.”

Legal experts from the start have said Manafort’s civil lawsuit faced an uphill battle.

The Justice Department’s regulations explicitly say that private parties have no right to challenge them in court. Judges in prior cases also have generally not permitted defendants in criminal cases like Manafort to use civil litigation to try to challenge criminal charges.

SCALED-BACK COMPLAINT

But Manafort’s case appeared to be even weaker in Jackson’s eyes on Wednesday after Downing told her he was scaling back the scope of the civil complaint against the Justice Department.

Manafort’s lawsuit originally asked the judge to declare that Rosenstein’s entire order appointing Mueller was invalid and to set aside the criminal charges against him.

On Wednesday, Downing said he is only challenging a portion of Rosenstein’s order, and that he is not asking the judge to toss the charges in this case, but instead seeking to protect his client from potential future charges also unrelated to Russia.

That prompted Jackson to ask an array of questions, including how Manafort can have legal standing to challenge the order if he has not suffered any harm, how he can know for sure whether or not Mueller may bring future charges within the proper scope of Rosenstein’s order, and whether there was legal precedent allowing someone to challenge a prosecution under the Administrative Procedure Act.

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“It seems to me you are trying to have it both ways,” she said, adding that Downing is not trying to dismiss the indictment but still has a problem with Manafort being prosecuted.

Downing told the judge Rosenstein’s order violates the rules governing special prosecutors because it lets Mueller broadly investigate “any matters that arose or may arise directly from” the probe into Russian interference.

He stressed that Manafort never even had an office in Russia and that the criminal case against him dates back to 2014, well before the campaign.

A court filing on Monday appeared to somewhat undermine that claim by showing that Rosenstein specifically authorized Mueller in August 2017 to investigate both whether Manafort colluded with Russia to interfere with the 2016 presidential election and his activities prior to 2016 involving Ukraine’s former pro-Russia government.

Jackson also is handling the criminal case against Manafort and is expected to hear oral arguments for that later this month, when Downing will ask her to dismiss the indictment.