The Department of Justice (DOJ) on Thursday filed a notice of intent to appeal a ruling by a judge granting former President Trump’s request for a special master, asking the judge to partially stay a ruling blocking them from accessing the classified materials seized during a search of his home.

“Without a stay, the government and public also will suffer irreparable harm from the undue delay to the criminal investigation,” the DOJ writes in its filing.

“Any delay poses significant concerns in the context of an investigation into the mishandling of classified records.”

The motion for a partial stay would allow the government to continue its review of the classified records recovered from Trump’s home, removing from review by a yet-to-be-appointed third-party special master some 100 documents of roughly 10,000 taken in the Aug. 8 search.

The appeal itself will continue to the 11th Circuit Court of Appeals, which includes six Trump appointees on the bench.

The filing digs into District Judge Aileen Cannon’s logic on a number of areas, pointing to many of the same issues in a ruling legal scholars largely panned as troubling.

But the bulk of the argument for a partial stay of her ruling granting a special master relies on the impact her decision could have on national security. 

Cannon allowed an intelligence community-led review of the documents to continue so that national security leaders could work to mitigate any fallout from the mishandling of records.

But the DOJ’s brief argues the intelligence community’s damage assessment and its own criminal investigation “are inextricably intertwined.”

“The ongoing Intelligence Community (“IC”) classification review and assessment are closely interconnected with—and cannot be readily separated from—areas of inquiry of DOJ’s and the FBI’s ongoing criminal investigation,” they write, taking pains to note that “the FBI itself is a part of the intelligence community.”

The intelligence community has had access to an earlier tranche of records turned over by Trump since May, after the National Archives recovered 184 classified documents from Mar-a-Lago in January.

“Before the Court’s Order, the same personnel from the FBI involved in the criminal investigation were coordinating appropriately with the IC in its review and assessment,” DOJ wrote, adding that the order “frustrate[s] the government’s ability to conduct an effective national security risk assessment and classification review and could preclude the government from taking necessary remedial steps in light of that review—risking irreparable harm to our national security and intelligence interests.”

DOJ even specifically points to the 48 empty folders with classified banners as well as another 42 empty folders that were labeled “return to staff secretary/military aide” that were recovered during the search of Mar-a-Lago.

It is the FBI, they say, that would typically carry out an investigation into such a matter.

“Within the United States, the FBI would pursue any allegation or lead indicating that the classified records may have been accessed, retained, or disseminated in violation of the law, including by using the tools and authorities of a criminal investigation,” the filing states.

“If, for example, another department or agency in the IC were to obtain intelligence indicating that a classified document in the seized materials might have been compromised, the FBI would be responsible for taking some of the necessary steps to evaluate that risk.”

The filing includes a declaration from Alan Kohler, assistant director for the Counterintelligence Division of the FBI, backing DOJ’s argument and calling the two investigations “inextricably linked.”

DOJ’s filing comes ahead of a Friday deadline to work with Trump’s legal team to propose a list of candidates to serve as the special master responsible for reviewing the documents. Cannon directed Trump’s team to consider DOJ’s position in their Friday filing and to respond to it fully by 10 a.m. Monday.

Elsewhere in the motion for a stay, DOJ picks apart the argument that Trump would have any executive privilege claims to classified records.

“The classification markings establish on the face of the documents that they are government records, not Plaintiff’s personal records. The government’s review of those records does not raise any plausible attorney-client privilege claims because such classified records do not contain communications between Plaintiff and his private attorneys. And for several reasons, no potential assertion of executive privilege could justify restricting the Executive Branch’s review and use of the classified records at issue here,” DOJ argued.

“There is no valid purpose to be served by a special master’s review of classified materials.”

DOJ also noted that Trump’s legal team never raised the concept of being able to claim executive privilege over any classified records after Trump’s custodian of records was subpoenaed in May and asked to turn over any remaining documents. 

“To the extent that Plaintiff believed that any such records could be subject to a valid assertion of executive privilege, he should have advised the government of such a claim at that time and could have attempted to pursue such a claim through a motion to quash. But despite having several weeks to respond to the subpoena, plaintiff did not do so,” DOJ wrote.

Trump mocked the appeal on his social media platform, saying that DOJ was “going to spend Millions of Dollars, & vast amounts of Time & Energy, to appeal the Order on the ‘Raid of Mar-a-Lago Document Hoax,’ by a brilliant and courageous Judge whose words of wisdom rang true throughout our Nation.”

DOJ’s appeal of the ruling came after many legal experts said they had but little choice to fight the decision, even if additional litigation could also drag out its ability to reinitiate review of classified records in a crucial step for its investigation. 

Barbara McQuade, a former U.S. attorney, said if the Justice Department’s primary goal is to indict Trump, an appeal could slow that process. But if DOJ decides the main goal is to protect executive privilege and its limitations from the potential precedent set by Cannon’s ruling, then a challenge makes more sense.

“They may need to appeal even if it means adverse impact on this particular case,” she told The Hill prior to DOJ’s filing.

As DOJ officials wrestled with the question of how to proceed, they even got a huge nudge from Bill Barr, Trump’s former attorney general, who came out sharply against Cannon’s ruling and urged the Justice Department to appeal it.

“The opinion, I think, was wrong, and I think the government should appeal it. It’s deeply flawed in a number of ways,” Barr said during an appearance on Fox News on Tuesday.

“Her decision is premature. And the dispute isn’t over whether this document is potentially executive privilege and this one isn’t. That’s not the dispute. The dispute is whether the president – even if it is executive privilege – can the president bar DOJ from reviewing the documents? And the answer to that I think is clearly no.”

Whatever the outcome of the DOJ’s challenge, some legal experts said the delay brought about by Cannon’s decision is already benefiting the former president.

“Delay is sweet for a prospective criminal defendant, especially a prospective criminal defendant who doesn’t seem to have any defense,” Jeff Robbins, a former federal prosecutor and congressional investigative counsel, told The Hill.

Mike Lillis and Morgan Chalfant contributed.

Updated at 8:33 p.m.