In 2015, the Intercept started publishing "The Drone Papers," based on classified documents leaked by an unknown whistleblower. Today, someone who worked at the NSA, and then at the National Geospatial-Intelligence Agency, was charged with the crime. It is unclear how he was initially identified. It might have been this: "At the agency, prosecutors said, Mr. Hale printed 36 documents from his Top Secret computer."
The article talks about evidence collected after he was identified and searched:
> According to the indictment, in August 2014, Mr. Hale's cellphone contact list included information for the reporter, and he possessed two thumb drives. One thumb drive contained a page marked "secret" from a classified document that Mr. Hale had printed in February 2014. Prosecutors said Mr. Hale had tried to delete the document from the thumb drive. > > The other thumb drive contained Tor software and the Tails operating system, which were recommended by the reporter's online news outlet in an article published on its website regarding how to anonymously leak documents.