Journalist Audrey Hudson grabbed files from the shelf behind her and set them on her desk. The chaos of boxes stacked on the white rug in her home office was a reminder of the pre-dawn raid by armed state and federal investigators nearly three months ago.

On Wednesday’s season finale episode of TheBlaze TV’s For The Record  (8:30 p.m. ET), we expose the government’s post-9/11 war on journalists in “The Silencer.”

TheBlaze visited Hudson’s home where she was still reeling from the events of Aug. 6, when officers stormed her home in Shady Side, Md., guns drawn. Her private notes — sacred to any reporter — with information about confidential sources and her thoughts and constructs of her investigations into failures at the Federal Air Marshal Service were confiscated by a Department of Homeland Security employee who accompanied police.

Never in My Wildest Dreams Thought Something Like That Could Happen in This Country: For The Record Exposes the Attempt to Silence Whistleblowers

Journalist Audrey Hudson had stacks of sensitive notes and information confiscated from her home during a raid by state and federal officers. (Sara Carter/TheBlaze)

Coast Guard investigator Miguel Bosch, a former air marshal, was with Maryland State Police on a warrant to search the house for weapons. The search warrant was issued for Hudson’s husband, Paul Flanagan, a longtime employee with the U.S. Coast Guard. He was found guilty in 1986 of resisting arrest and cannot possess firearms. But Hudson said Bosch was there to search for more than weapons, and he let her know exactly who he was. Hudson said she didn’t realize what exactly had happened until more than a month later, when she received a notice to come collect her files and paperwork from the Coast Guard.

“He let me know that he was once with the Federal Air Marshals,” Hudson, an award-winning former reporter with The Washington Times, told TheBlaze. In 2004, she exposed that the Federal Air Marshal Service and Transportation Security Administration had lied to Congress and that less than 5 percent of airline departure flights in the U.S. were being protected.

“I now know why he was spending so much time in my upstairs office … horrified doesn’t even begin to describe — but this shook me to my core, I was almost paralyzed,” she said. ”I never in my wildest dreams thought something like that could happen in this country.”

Hudson is one of hundreds of reporters and civilian personnel that the U.S. Department of Justice and Department of Homeland Security have investigated or threatened with investigation. Earlier this year, the Associated Press discovered that prosecutors working for Attorney General Eric Holder had collected phone logs for 20 AP phone lines used by more than 100 reporters and editors. Holder’s prosecutors also seized phone records of several AP journalists, and the attorney general personally approved a warrant to obtain emails and phone records for Fox News reporter James Rosen, including Rosen’s parents’ phone records. They labeled Rosen a “criminal.”

Coast Guard spokesman Carlos Diaz told TheBlaze that when the warrant was being carried out, Bosch “discovered government documents labeled ‘FOUO’ – For Official Use Only and ‘LES’ – Law Enforcement Sensitive” — documents that were considered government property.

The “files that contained these documents were cataloged on the search warrant inventory and taken from the premises and remained in the custody of the Maryland State Police and remained in the custody the MDSP and the Coast Guard Investigative Service,” Diaz said.

He said that once the documents were reviewed and confirmed that they had been obtained through a Freedom of Information Act request, they were cleared and Hudson was notified to retrieve them.

But Diaz could not explain why they confiscated the documents when attached to the front page was a Freedom of Information Act letter confirming that they had been rightfully obtained.

John Malcolm, a senior legal fellow at the conservative Heritage Foundation’s Center for Legal & Judicial Studies, called the actions in Hudson’s case “highly suspicious” on the part of Homeland Security. He said sending Bosch, who was once an officer with the agency Hudson had investigated, sends a “chilling effect to any reporter” working on investigative stories.

Malcolm said that while investigators were officially there looking for guns and ammunition, they spent the majority of time in Hudson’s private office and took not only law enforcement documents obtained legally, but her private notes, telephone numbers and notebooks.

“They had pulled out every box from my closet,” said Hudson, who said they confiscated five complete files on her series of air marshal stories but no other files among the hundreds in her closet. “I haven’t finished putting them back. They’re just sitting here.”

When Homeland Security “seized Ms. Hudson’s typewritten and handwritten notes – notes that happen to contain the names of confidential sources” who accused officials working for the department of lying to Congress, “it’s possible they violated Ms. Hudson’s Fourth Amendment rights by exceeding the scope of the warrant and seizing evidence that was totally unrelated,” Malcolm said.

John Solomon, executive editor at The Washington Times who worked with Hudson on her stories, is now considering a lawsuit against Homeland Security for violating Hudson’s rights.

Hudson is still struggling with the events of the raid. She is worried that Homeland Security sources she spoke with during her investigations will face retribution or others she may never have spoken with, but whose names are contained in her personal notes, will also come under fire.

“I feel sick to my stomach everyday since the incident,” Hudson said. “It’s not just about what happened to me – it’s about our nation, our rights and freedom. How can we be the watchdogs when our government has now crossed the line. Who’s going to trust us when we can’t protect our sources?”

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