“I don't intend that aspect to delay this aspect of it,” Breyer said. The judge, who handled a shareholder lawsuit over related issues that settled in 2015, said the legal fallout from the merger has taken unexpected twists. “It goes in directions that I'm not sure I would've anticipated.”

Tim Crudo, a former federal prosecutor turned defense lawyer, said Hussain's not guilty plea was expected. Any deal he might have worked out to cooperate with the government and testify against Lynch would have required a guilty plea and probably would have been negotiated before he was indicted, Crudo said.

'Scrubbing This'

“The government has been scrubbing this thing for a long time,” Crudo said. “I'm sure there have been discussions. Had they been able to work out a deal, they would've done it.”

Crudo said prosecutors probably had to reach an agreement with Hussain for him to waive a deadline for bringing charges within five years of the alleged offense. Unless the government can allege that some conduct occurred within that time period, it would be hard-pressed to pursue a case against Lynch and other Autonomy executives unless they, too, have privately consented that it's not too late to prosecute them under the statute of limitations, he said.

Hussain's lawyer, John Keker, declined to comment after Thursday's hearing. He previously said it was a “shame” the U.S. Justice Department was doing Hewlett-Packard's bidding by charging him. Keker told the judge in December he expected the case against Hussain to go to trial.

Assistant U.S. attorneys Robert S. Leach and Adam A. Reeves also declined to comment after the hearing.

After he was indicted, Hussain agreed to post bail of $1,000 and has been allowed to stay at home in England and travel so long as he doesn't visit a country that doesn't have an extradition treaty with the U.S.

Hussain is still working with Lynch, who runs a Europe-focused $1 billion venture capital firm, Invoke Capital, that invests in tech startups and also helps set up and manage them.

Insufficient Evidence

The U.K.'s Serious Fraud Office has said there was insufficient evidence for a prosecution of Autonomy officials. In the U.S., Christopher Egan, the former chief executive officer of Autonomy's U.S.-based subsidiary in San Francisco, agreed in November to pay $923,000 to settle an administrative proceeding in which the Securities and Exchange Commission accused him of participating in an accounting scheme. Egan, who left the company in November 2012, didn't admit or deny the regulator's findings.

Hewlett-Packard's acquisition of Autonomy came before a split of the company in 2015 that created Hewlett Packard Enterprise Co., which focuses on technology for data centers, and HP Inc., which sells computers and printers.

Hewlett Packard Enterprise has since been looking to shed other assets. The company last year announced it was spinning off and merging some non-core software assets in a multibillion-dollar deal with U.K.-based Micro Focus International Plc. As part of that deal, Micro Focus will be picking up pieces of Autonomy.

This case is U.S. v. Hussain, 16-cr-00462, U.S. District Court, Northern District of California (San Francisco).

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