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AP Photo/Seth Wenig

A U.S. district judge wants to determine why Uber failed to turn over some explosive evidence as it battled a lawsuit alleging it stole self-driving car secrets.

Judge William Alsup, overseeing the case brought against Uber by Waymo, the self-driving car unit of Google parent company Alphabet, said Uber could have innocently overlooked the evidence. But if he finds that Uber engaged in “systematic concealment of evidence,” Alsup plans to tell the jury “about these problems, all of Uber’s making,” he said at a hearing on Dec. 4 in federal court in San Francisco.

The evidence in question consists of two documents: a 37-page demand letter written in May by a lawyer for former Uber security analyst Ric Jacobs, and Jacobs’ resignation email, sent to top Uber executives a month earlier.

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Both letters allege that Uber engaged in clandestine practices, including theft of trade secrets. They came to light in late November when the U.S. attorney’s office for the Northern District of California sent Jacobs’ lawyer’s letter to Alsup, who had previously referred the case there for possible criminal investigation.

The revelations, a potential smoking gun, threw the lawsuit into turmoil, causing Alsup to delay the planned jury trial until Feb. 5.

“This is not the usual case,” Alsup said. “There’s been a lot of this destruction of evidence; a lot of what looks like hide the ball — but not necessarily. Some of it could have been innocent.”

Hearing allegations that Uber destroyed evidence could influence the jury’s deliberations. “If both sides are playing fair and square, and there are none of these issues, then you get to decide the case strictly on its merits; you don’t get off into destruction of evidence,” Alsup said.

Alsup assigned the special master in the case, John Cooper, to investigate and report back by Dec. 15 whether the ways Uber and Waymo had requested discovery should have turned up the Jacobs letters, which he called “highly inflammatory, highly material documents.”

Cooper’s probe will also cover whether Jacobs’ settlement agreement should have been turned over. Uber paid Jacobs $4.5 million on top of $3 million to his attorney, though Uber associate general counsel Angela Padilla disparaged him in court last week as an “extortionist” making “fantastical” accusations. Jacobs is currently working for Uber as a $1 million-a-year consultant, whose duties revolve around investigating the claims in his letter. His consulting fee is part of his $4.5 million payout from the ride-hailing company.

Jacobs alleged Uber used a variety of tactics, including self-destructing emails and non-attributable devices to cover its tracks. Alsup gave Uber permission to interview former Waymo employees now working at Uber about whether Waymo used similar tactics.

Google, Waymo’s sister company, makes several products, including Google Chat, Hangouts and Allo, that allow for ephemeral communications.

Alsup is concerned that ephemeral messaging could have destroyed documents that would have been relevant in the case.

If Uber says it could not find stolen trade secrets on its servers, “It’s a very good answer to come back and say, ‘No, we learned they had an ephemeral system, a shadow system, a clandestine system where they destroyed everything after six minutes or six days and that helps explain why they weren’t on the server,’” Alsup said.

Alsup already postponed the jury trial once before. That delay stemmed from Uber’s late production of documents Waymo had requested about its acquisition of Otto, a self-driving truck company started by Anthony Levandowski, a former Waymo star engineer who Waymo says stole sensitive data and brought it to Uber.