Assistant US Attorney Jennifer Solari said agents searching Winner's home found handwritten notes in several languages, including one that said, "I want to burn the White House down," ABC News and The Augusta Chronicle reported.
Her social media accounts had revealed a deep dislike of President Donald Trump, with one post calling him "the orange fascist."
Other notes found at her home included details on how to access the "dark web," set up a burner email account and listed the names of Taliban leaders, news reports said.
Winner, who worked for NSA contractor Pluribus International Corporation in Augusta, Georgia, was a specialist in Pashto, Farsi and Dari, languages spoken in Afghanistan, Iran and Pakistan, her mother has said.
Solari warned that Winner may possess more stolen secrets.
Judge Brian Epps denied bail, meaning Winner will stay behind bars until trial, after Solari said some of the evidence was "downright frightening."
Her lawyer Titus Nichols rejected that characterization, saying his client has no history of violence. He said his Winner is just a millennial comfortable with technology.