After Mr. Jacobs left Uber, his lawyer sent the 37-page letter to Ms. Padilla as part of settlement negotiations in May. Ms. Padilla said the company had not shared this letter with the legal team handling the Waymo case because Uber hadn’t wanted to compromise an internal investigation into its claims.

Judge Alsup said to Ms. Padilla that “on the surface, it looks like you covered this up” and tried to keep the letter out of the hands of Waymo’s lawyers.

The company did share the letter from Mr. Jacobs’s lawyer with three different United States attorney offices, because Mr. Jacobs had threatened to take his claims to federal prosecutors and Uber wanted to “take the air out of his extortionist balloon,” Ms. Padilla testified.

Nonetheless, Uber paid a $3 million settlement to the lawyer who wrote the letter in addition to the $4.5 million paid to Mr. Jacobs. As part of the deal, Mr. Jacobs was kept on as a security consultant, Ms. Padilla testified. His job: investigating the claims made in the letter his lawyer wrote.

Mr. Jacobs received $2 million up front and was to receive $1 million spread over 12 months and $1.5 million in stock, also spread out over 12 months. The deal included a so-called clawback measure that would require him to return the money if he discussed his claims with outsiders, Ms. Padilla testified. But he was allowed to talk about it with the government in the case of an investigation.

On Wednesday, two current Uber security employees denied many of the allegations in the 37-page letter and claims by Mr. Jacobs in his testimony on Tuesday. But they acknowledged that Uber employees used a so-called ephemeral messaging app called Wickr. Uber’s current chief executive, Dara Khosrowshahi, noted the company’s use of Wickr in a tweet but said Uber had stopped using it.

Both security employees also testified that Mr. Levandowski had used the messaging service, but that they did not know what he had used it for.