WASHINGTON (CN) – Adding a new wrinkle to litigation over the 2012 U.S. consulate attack in Benghazi, Libya, a federal judge put a spotlight Wednesday on emails sent by three aides to then-Secretary of State Hillary Clinton.

“This matter is a far cry from a typical FOIA case,” the ruling by U.S. District Judge Amit Mehta says, abbreviating Freedom of Information Act. “Secretary Clinton used a private email server, located in her home, to transmit and receive work-related communications during her tenure as secretary of state.”

Mehta is presiding over a case in Washington filed two years ago by the conservative group Judicial Watch.

Though the State Department searched outside for records responsive to the Judicial Watch request, Mehta said it has yet to search its own email server.

He agreed with the watchdog Tuesday that the agency must search the state.gov email accounts of three former Clinton aides: former chief of staff Cheryl Mills, former deputy chief of staff Huma Abedin, and former director of policy planning Jacob Sullivan.

“If Secretary Clinton sent an e-mail about Benghazi to Abedin, Mills, or Sullivan at his or her state.gov e-mail address, or if one of them sent an e-mail to Secretary Clinton using his or her state.gov account, then State’s server presumably would have captured and stored such an e-mail,” the 10-page ruling states. “Therefore, State has an obligation to search its own server for responsive records.”

Ramona Cotca, the filing attorney for Judicial Watch, said government agencies typically search their own records first.

“That’s what has had us puzzled, and the great lengths its gone to,” Cotca said in a phone interview. “And the briefing, I mean this has been a process of over a year between the time we had briefing scheduled and by the time we briefed everything.”

The State Department’s previous search of 30,000 emails Clinton had provided to the agency in 2014 produced 342 records responsive to Judicial Watch’s FOIA request.

After asking the three Clinton aides to turn over emails and other records that were sent or received using a personal email account, the department turned up one more responsive record.

Mehta’s ruling says the State Department also searched emails from Clinton’s personal email server, which the FBI recovered during its investigation. In total, the department has turned more than 348 records to the conservative watchdog, 125 of which were produced in full.

Judicial Watch attorney Cotca called the ruling “correct,” and said she is “very happy” with it.

“It’s been surprising to me that the State Department has fought this hard just for something so basic, to search official email accounts with respect to the Benghazi attack,” she said. “But I think Judge Mehta definitely did the right thing. It’s not about how many records, but it’s a matter of making sure that they search everywhere where they’re supposed to search.”

The State Department did not immediately respond to an emailed request for comment about the opinion.

Cotca said both parties must file a joint status report by Sept. 22, at which point the State Department must update the court on the progress of its search of the state.gov email server.