Harold Thomas Martin III, 52, faces 20 counts of willful retention of national defense information.
The indictment alleges Martin removed classified documents from 1996 to 2016. He is accused of keeping documents in his home or car.
The documents include highly classified materials from the National Security Agency, the US Cyber Command, the CIA and the National Reconnaissance Office. Among the documents are ones that reveal US military gaps, capabilities and operations, as well as ones that contained foreign intelligence collection methods, targeting information and technical user materials.
Martin's attorney had no comment when contacted by CNN.
FBI investigators haven't concluded what Martin's motivation was for stealing the documents. At a hearing in late October a public defender representing Martin said his client was a hoarder who was "completely out of control."
Information found in his car
Before his arrest in August, Martin worked as a contractor to the National Security Agency through consulting firm Booz Allen Hamilton, which fired him after he was charged. He has a long history working with sensitive government intelligence, and served in the US Navy and Naval Reserves for more than 10 years, reaching the rank of lieutenant.
The information he had digitally in his car, the feds said, was equivalent to approximately 50,000 gigabytes, enough to store 500 million documents containing images and text.
The government said Martin had a document "regarding specific operational plans against a known enemy of the United States and its allies." That document was not only classified but marked need-to-know only, and Martin should not have been privy to that information, prosecutors said in court filings.
Also found were files containing personal information of government employees, and an email chain with "highly sensitive information" on the back of which were handwritten notes "describing the NSA's classified computer infrastructure and detailed descriptions of classified technical operations."
Among the documents the FBI believes Martin stole were some detailing a hacking tool that the NSA developed to break into computer systems in other countries, law enforcement sources said when he was arrested. Documents detailing the tools were posted on the Internet in recent months, though no connection to Martin has been offered.
Martin's attorneys have argued previously in court that he is not a flight risk because he does not have his passport and has a wife and home in Maryland. They noted his military service.
Martin will make his next appearance in court on February 14.