Hillary Clinton is good at imagining partisan plots, and to listen to her team, no less than several inspectors general, the intelligence community, and the entire Republican ecosphere are colluding to turn her home-brew email system into a fake scandal. To this conspiracy, she must now add the federal judiciary.

In recent weeks, not one, but two, esteemed federal judges have granted an outside group—Judicial Watch—the right to conduct discovery into the origins and handling of her private email system. It’s a reminder that Mrs. Clinton’s biggest problem this election isn’t Bernie Sanders or Donald Trump. Her problem is a 1966 statute known as the Freedom of Information Act, and the judges who enforce it.

The judges have taken unprecedented steps to resolve this case. It is exceedingly rare—almost unheard of—for a judge to allow discovery in a FOIA proceeding. This is a testament to how grave Mrs. Clinton’s email problem is. In the usual course of things, an outside group demands documents, a judge requires a federal department to hand them over, and the public learns something.

In this case—as we all know—the problem is that the State Department doesn’t have the documents. Or rather, it can’t confirm that it has them all, because State left it to Mrs. Clinton and her aides to possess them, and then to unilaterally decide what to hand over. To Judge Royce Lamberth, this is cut and dry “evidence of government wrong-doing and bad faith,” and the law demands a full accounting of how this situation came to be, what records exist, and where they are now.

Speaking of the judge’s words, they too are a testament to Mrs. Clinton’s mess. Judge Lamberth was unplugged in his order, calling the former secretary of state’s email set up “extraordinary,” and slamming “constantly shifting admissions by the government and former government officials” about the setup. Judge Emmet Sullivan, the first to allow discovery, referred in his own hearing to Mrs. Clinton’s “totally atypical system” and noted that it “boggles the mind that the State Department allowed this circumstance to arise in the first place. It’s just very, very, very troubling.”

Fueling the judges’ suspicions has been new evidence that Mrs. Clinton didn’t turn everything over. Judicial Watch recently obtained emails showing that State Department and National Security Agency personnel had big concerns with Mrs. Clinton’s early demands that she be allowed to use a BlackBerry for secure correspondence. They wanted her to sit at a computer in a secure facility—as everyone else does. These documents include a February 2009 email from then-Clinton chief of staff Cheryl Mills to her boss, crowing that State was coming around to Mrs. Clinton’s demands, and a return email the same day from Mrs. Clinton saying, “That’s good news.”

These are clearly work-related emails. They speak to the question of Mrs. Clinton’s communications while at the State Department. They aren’t about yoga routines. And yet, guess what? That email chain was not included in the 55,000 pages of documents Mrs. Clinton turned over. Perhaps it was an oversight, but far more likely, the Clinton team—knowing the firestorm over a home-brew system—chose to withhold documents showing that State and NSA considered Mrs. Clinton’s email demands unsafe and unreasonable. What else did Mrs. Clinton choose to withhold from the public?

One other aspect of these new emails: Mrs. Clinton sent her “good news” email to Ms. Mills via her private hdr22@clintonemail.com account in February 2009. And yet the former secretary of state has publicly claimed she didn’t start using that address until March 2009, well after she was sworn in as secretary of state.

Judicial Watch is hoping to use discovery to interview eight current and former State Department officials, including Ms. Mills, Clinton aide Huma Abedin, top State Department official Patrick Kennedy, and former State IT employees Bryan Pagliano (who is reported to have recently been granted immunity by the FBI). And yet in a hearing this week in Judge Sullivan’s court, State Department officials were already moving to limit or shut down what questions Judicial Watch could ask—including those pertaining to how classified information was handled on the system.