The ex-CIA software engineer suspected of leaking a massive, highly secret trove of U.S. hacking tools and source code to WikiLeaks has been charged in federal court with a series of Espionage Act violations.

Joshua Schulte, 29, allegedly disclosed thousands of top-secret files outlining the extent of the CIA’s cyberwarfare capabilities in an unprecedented breach that triggered an intensive investigation even before WikiLeaks published the information in March 2017.

In March and June 2016, Schulte modified a computer run by the U.S. Intelligence Agency to “delet[e] records of his activities” and “den[y] others access to the system,” prosecutors charge in a superseding indictment unveiled Monday.

The former CIA engineer was accused formally in the indictment of lying to federal investigators, illegally gathering and transmitting national security information, theft of government property, and other offenses.

“As alleged, Schulte utterly betrayed this nation and downright violated his victims,” assistant New York FBI field director William F. Sweeney, Jr., said in a statement. “As an employee of the CIA, Schulte took an oath to protect this country, but he blatantly endangered it by the transmission of Classified Information.”

Schulte was charged last year with knowingly receiving and possessing child pornography, and those charges are also listed in the latest federal grand jury indictment.

WIKILEAKS RELEASES THE ‘ENTIRE HACKING CAPACITY OF THE CIA’

Prosecutors signposted the new charges weeks ago, even as his defense team accuses the U.S. of scapegoating.

“As the evidence is flushed out, it will become clear that Mr. Schulte is hardly the villain the government makes him out to be,” Sabrina P. Shroff, Schulte’s public defender, said in a statement Monday.

A CIA spokesperson said in a statement: "We are grateful to the Department of Justice, and others throughout the government, who worked diligently to bring this indictment in connection with a grave breech of national security."

In a strange twist, while he was still working with the CIA, Schulte reportedly tweeted that WikiLeaks source Chelsea Manning should be killed for her disclosures.

“Kill the prick,” he reportedly said on Twitter in response to a story about Manning.

Last March, WikiLeaks touted its stunning 8,000-plus page disclosure as the full hacking capacity of the CIA, saying it was “the largest ever publication of confidential documents on the agency.”

The 8,761 documents and files — released as ”Vault 7 Part 1,” and titled “Year Zero” — were obtained from an “isolated, high-security network” at the CIA’s Center for Cyber Intelligence in Langley, Va., WikiLeaks claimed.

Prosecutors charge that Schulte committed the crimes in Virginia, where the CIA is headquartered.

Fox News’ Cody Derespina contributed to this report.