The arrest of Harold Martin was announced in October 2016. He was working for Booz Allen Hamilton at the time of his arrest.
But the terms of the deal mean that Martin has no guarantee that he will not face 19 additional felony charges.
This document is said to be "a March 2014 NSA leadership briefing outlining the development and future plans for a specific NSA organisation".
"The information contained within this document related to United States military and naval establishments and related activities of national preparedness, as well as the defence of the United States against its enemies," according to prosecutors.
Charges over 12 other NSA documents will remain in place.
But equally, a third NSA ex-worker, Nghia Hoang Pho who pleaded guilty to taking national defence information home, is also suspected of being the Shadow Brokers' source.
Martin was a member of the Tailored Access Operations group of the NSA, an elite hacking unit, as was Pho.
After the leaks by NSA contractor Edward Snowden in 2013, three people are known to have been involved in unauthorised removal of NSA material from the agency.
One is Martin. The second, Pho, was, before his guilty plea, identified in the media as an unnamed software developer who was a Vietnamese American. He was taken into custody in 2015 after taking hacking tools home.
The third person, a woman named Reality Winner, was arrested after leaking a single NSA document to The Intercept this year.
Martin's lawyer, the federal public defender Jan Wyda, claimed at the first hearing in October 2016 that he was no traitor, only "a compulsive hoarder".