SAN FRANCISCO—US District Judge William Alsup has delayed an upcoming trial, Waymo v. Uber, in which Alphabet’s self-driving car division has accused Uber of massive data theft.

The postponement came as a former Uber security employee, Richard Jacobs, made startling accusations in court Tuesday about his former colleagues’ tactics of what he dubbed "overly aggressive and invasive" actions, including seeking code accidentally made available on GitHub and internal use of "ephemeral and encrypted" communications including through Wickr and "non-attributable machines."

The case began back in February, when Waymo sued Uber and accused one of its own former employees, Anthony Levandowski, of stealing 14,000 files shortly before he left Waymo and went on to found a company that was quickly acquired by Uber. The case will likely have a huge impact on the future of autonomous vehicles and who will emerge dominant in the field.

The lawsuit has been thrown into chaos as federal prosecutors suddenly—and highly unusually—sent a still-sealed November 22 letter to the judge about their investigation. Judge Alsup had previously referred possible criminal behavior by Uber to be examined by prosecutors. In a public Monday evening filing, Waymo asked that the trial date be put off.

The letter from the United States Attorney’s Office refers to what has been dubbed the "Jacobs Letter," written in May 2017 by Clayton Halunen, a Minnesota lawyer who represented Richard Jacobs. Jacobs worked for Uber’s Strategic Services Group, a now-disbanded secretive intelligence division within the company. Both letters remain non-public, for now.

This confidential demand letter came about in the context of a threatened lawsuit, which seemingly never materialized. Ultimately, Jacobs was paid a previously undisclosed $4.5 million settlement. A Tuesday evening filing by Jacobs' new lawyer, Martha Boersch, asked the judge keep the entire letter confidential.

Waymo wrote in its Monday filing that the new revelations demand "further detailed and lengthy investigation to discover the extent to which [redacted] in the Jacobs Letter relates to Waymo’s trade secret claims and spoliation arguments here."

"You don’t get taught how to deal with this problem in law school," Alsup said during the Tuesday hearing. "In 25 years of practice and 18 years in this job I have never seen such a problem."

Alsup then immediately called for Jacobs to take the stand for an evidentiary hearing, which he did.

Charles Verhoeven, Waymo’s head lawyer, began questioning Jacobs about that letter, quoting from one portion that read, "Jacobs is aware that Uber used the MA [Marketplace Analytics] team to steal trade secrets at least from Waymo in the United States," and another portion, saying, "MA exists expressly for the purpose of acquiring trade secrets, code base, and competitive intelligence."

Marketplace Analytics is an Uber division that provides information about Uber’s "competitive landscape."

Jacobs eventually responded that he had not fully read his own lawyer’s letter: "I don’t think I did as thorough a job as I wish I could have," and disputed his lawyer’s characterization of his own activities and those of his colleagues as "hyperbolic."

However, Jacobs questioned Uber’s actions. The ex-employee said he left the company earlier this year. Jacobs remains a paid consultant to the company as a way of assisting investigations of previous wrongdoing at Uber.

It's not over

Judge Alsup said later in the hearing that he would seek to release the United States Attorney's letter, and gave federal prosecutors until 5:00pm Pacific Time to file any objections.

He also had strong words for Uber and its attorneys.

"I want Uber to supply all documents in the entire company that have anything to do with ephemeral, anything to do with non-attributable devices, and anything to do with false attorney/client privilege," he said. "We have to get more to the bottom of this shadow system that Uber set up and it may turn out to be nothing, but it may turn out to be an important way to conceal the testimony."

He then said that the evidentiary hearing would continue on Wednesday, where Uber's general counsel, Angela Padilla, would be ordered to testify.

"I’m just going to say to you: I would look like a fool if Uber were to fool me on this," the judge continued, addressing Uber's lawyer, Arturo González. "You told me many times that none of these documents never hit the server."

Gonzalez then said that he stood by that assertion.

"Well it turns out that the server is only for the dummies and the real stuff goes on the shadow system," Alsup continued. "It would just be wrong, it would be unfair not to give them a chance to [get this.] There’s enough under oath to believe that there is a 50-50 chance that this will be bad for uber and there’s a 50-50 chance that it will be a dry hole."

"Nobody on this defense team knew about this," González said.

"Somebody at Uber knew," Alsup retorted. "It helps me have more confidence in your team, but it doesn’t solve the Uber problem."

Alsup suggested that Uber hasn't been particularly straightforward during the course of the litigation.

"There are search terms in a protocol that two sides negotiated at the outset of the case," González added. "That is what we used."

"The server turns out to be for dummies, that’s where the stuff that doesn’t matter shows up. The stuff that does matter is going to be in the Wickr evaporate file.”

Alsup didn't mince words: "Any company that would set up such a surreptitious system is as suspicious as can be," adding "You’re making the impression that this is a total cover up.”

The judge ordered Uber to produce a list of all the employees that had, or used "Wickr or any other self-deleting communication systems.”

A new trial date has not been set.