"Anthony is innocent, and we look forward to proving it at trial", said the lawyers. Emails and texts revealed a deeply personal connection between Levandowski and Uber's then-chief executive officer, Travis Kalanick. Levandowski, though, had already surrendered both passports to the Federal Bureau of Investigation and will be required, at least initially, to wear an ankle bracelet with Global Positioning System tracking. A prosecutor expressed concern at the arraignment that Levandowski might be a flight risk.
Levandowski is facing a prison sentence and a fine if convicted.
During the last month before he quit Google, Levandowski downloaded 14,000 files containing "critical engineering information about the hardware" used by Waymo's self-driving vehicles from the company's internal Google Drive.
Although Tuesday's indictment did not charge Uber, it is a stain for a company that has been trying to recover from a series of scandals since jettisoning Mr Kalanick two years ago.
"All of us have the right to change jobs", United States Attorney David L. Anderson said Tuesday in a statement, according to NBC News.
Anderson declined to answer a reporter's question on whether Uber could also face any criminal charges. One that no other company would have.
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Until 2016, Levandowski worked on Google's self-driving auto initiative, Project Chauffeur - later dubbed Waymo.
Anthony Levandowski was once one of Silicon Valley's most sought-after technologists.
Levandowski, a pioneer in robotic vehicles, was charged with 33 counts of trade secret theft.
Following his departure from Uber, Levandowski co-founded another autonomous driving startup, Pronto.
Uber suspended its autonomous vehicle testing on public roads after the crash, and it was also put on hold by Arizona's governor. Reports suggest, the 39-year old has been accused of 33 counts of trade theft which also involves Alphabet's self-driving auto technology. That lawsuit alleged a "striking resemblance" between some of Waymo's designs and Uber's, singling out Levandowski as the thief. Uber feared it would face a cost disadvantage if another company started an autonomous ride-hailing service first.
Prosecutors said there remain legal limits to competition. "These are heavily protected confidential information and accessible on a need to know basis", said Federal Bureau of Investigation agent John Bennett. "The fast pace and competitive environment does not mean federal laws don't apply or they can be ignored". "We would want this intelligence to say, 'Humans should still have rights, even though I'm in charge'".
Alphabet shares closed down 36 cents at $1,170.82, while Uber fell 20 cents to $33.11.