A federal judge on Wednesday appeared skeptical of a civil lawsuit filed by former Trump campaign chairman Paul Manafort alleging that the Justice Department and Special Counsel Robert Mueller exceeded their authority in prosecuting him as part of the sprawling Russia probe.

The judge, Amy Berman Jackson, is also presiding over the criminal case brought by Mueller against Manafort in federal court in Washington, D.C. (There’s an additional criminal case against Manafort pending in Virginia). Manafort is facing charges of tax fraud, bank fraud, money laundering and failing to disclose foreign lobbying related to his work in Ukraine. He has pleaded not guilty.

Over the course of Jackson’s tough questioning of Manafort attorney Kevin Downing, Downing seemed to narrow what he was seeking with the lawsuit, which had already been whittled down since the initial complaint was filed.

“I don’t really understand what’s left to your case,” Jackson said during a hearing on motions related to the civil case, including DOJ’s request that the lawsuit be dismissed.

Manafort, in the civil lawsuit, attacked Mueller’s prosecution on two fronts. He is challenging the initial special counsel appointment order issued by Deputy Attorney General Rod Rosenstein (who is overseeing Mueller’s probe because Attorney General Jeff Sessions has recused him). His is also challenging Mueller’s actions pertaining to Manafort, arguing that because the indictments focus on work Manafort did before the 2016 campaign, they are beyond the scope of the Russia investigation.

The lawsuit initially seemed to seek that the indictments be thrown out, but Downing has since agued that that’s not what Manafort was asking for. At Wednesday’s hearing, Downing also said that he was no longer pursuing the second count — focused on Mueller himself — and that the lawsuit was just challenging the appointment order. He also said that he wasn’t challenging the entire appointment order, but a bulletpoint allowing Mueller to investigate “any matters that arose or may arise directly from the investigation,” which Downing said violated the Administrative Procedure Act.

“Nobody challenges prosecutions under the APA,” Jackson said while questioning Downing. “Do you have case that supports this?”

Downing later said he did not know if he had such a case.

The Justice Department, which was represented by career attorneys (though members of Mueller’s team were present in the courtroom), argued that a civil lawsuit is not the appropriate place to bring issues with Mueller’s investigation that instead could be brought in the criminal cases against Manafort.

DOJ attorney Daniel Schwei said that if Manafort could use the APA to challenge the appointment order, it would open the door to APA lawsuits challenging agencies any time they hire new employees for specific tasks — even before those employees take any actions.