I spent the early days of my 20-year army career working on newspapers that were read by soldiers, families and military retirees. “Command information,” we called it—which, broadly translated, meant “all the news the commanding general sees fit to print.” Our small staff worked long hours each week writing and editing stories about field training exercises, new uniform policies, and the latest pick for the officers’ wives book club. We were charmingly earnest about our job and burned gallons of the proverbial midnight oil each Tuesday night before the paper “went to bed,” en route to the printer.

For the most part, the colonels and generals were hands-off and allowed us to do the job we were trained to do.

I do recall one time, though, when a burly, red-faced command sergeant major became very hands-on. One of our journalists had referred to the post’s top enlisted soldier—first name, John—as “Johnny” in a photo caption. An hour after the newspaper hit the streets, the sergeant major roared into our office, got nose-to-nose with me, and shouted, “The only person who calls me ‘Johnny’ is my mother. And you, sergeant, are not my mother!”

We offered to print an apologetic correction in the next issue, but that wasn’t good enough for the sergeant major. He told us to immediately go out and retrieve all copies of the newspaper. And so, the entire public affairs staff hustled around to scoop up that week’s issue from the racks at the commissary, post exchange, hospital, and wherever else our 18-page newspaper could be found. Then the sergeant major ordered us to take an X-Acto knife to each issue, carefully cut out the “Johnny” reference, and re-distribute the paper across post. Because John was large and in charge, we complied.

My story is as quaint as a plate of Grandma’s brownies compared to the ongoing skirmish between U.S. Marine Corps Gen. Jim Amos and Marine Corps Times, a weekly independent publication with a circulation of about 36,000. This past December, following a series of articles published last May that held Amos accountable for his actions in a controversial court case, the order came down the chain of command to relocate the newspaper away from checkout lines at Marine Corps Exchange stores worldwide.

“We only found out about it when word trickled up to us from our distributors,” said Andrew deGrandpre, Marine Corps Times managing editor. “We took issue with the way it was done since we pay a premium to be in that checkout-line location.”

Though the publication is also sold in commissaries, Wal-Marts and some convenience stores near Marine Corps installations, deGrandpre said the bulk of their sales come from exchanges.

Those sales took a hit when copies of Marine Corps Times were moved from prime retail real estate to another, less-visible part of the store.

“The first thing I thought was, ‘This is questionable,’” deGrandpre told The Daily Beast.

The editor surmised that the reaction might be tied to the newspaper’s series of investigative reports that ran in May about how Amos allegedly abused his authority in a high-profile court case for a July 2011 incident involving Marines in Afghanistan. The top Marine general and four of his legal advisors were implicated in a complaint to the Defense Department Inspector General charging they inappropriately influenced the prosecution of cases stemming from the infamous video showing scout snipers urinating on dead insurgents in Afghanistan. That video had quickly gone viral on YouTube. “The complaint,” Marine Corps Times reported, “alleges Commandant Gen. Jim Amos, or others acting on his behalf, deliberately sought to manipulate the legal process, effectively stacking the deck against the scout snipers in the video.”

“The timing was certainly suspicious,” deGrandpre said. “We’d been writing these tough stories on the commandant and our initial question was: ‘Were we being punished?’”

While he couldn’t know for sure at the time of the newspaper’s disappearance in December, DeGranpre and his staff recently learned of an internal email discussion that occurred around the time of the series’ publication and confirmed his theory. It was a correspondence between Col. Chris Hughes, deputy director of Marine Corps public affairs at the Pentagon, and two senior executive service employees, Sheryl Murray, the assistant deputy commandant for Manpower and Reserve Affairs, and Robert Hogue, the commandant’s top civilian attorney. In it, Hughes complained about the newspaper: “Every couple of years, we have a falling out with Marine Corps Times that warrants consideration of some level of ‘ban’ from our facilities. We believe that we may be close to such an impasse, and we want to present the Commandant with options. We believe it becomes a ‘good order and discipline’ issue if [Amos] believes he is being misrepresented by them. On such grounds, could he prohibit their sale in our [Marine Corps Community Services] facilities? Or, could he place them somewhere less prominent?”

Murray wrote back to Hughes within half an hour, saying she’d discussed the matter with her boss, Lt. Gen. Robert Milstead, deputy commandant for Manpower and Reserve Affairs, whose command has responsibility for the exchange stores and commissaries on Marine Corps installations. “Chris,” Murray wrote, “I just discussed this with Gen. Milstead, and he says, ‘this is the dumbest idea he has ever heard and he will not entertain it.’”

Not long after that, Hogue emailed Hughes, saying, “I recommend we try to talk the boss off the ledge here. That said, to respond to your specific question, there are authorities we can use to move the MCT from a position of prominence in our facilities.”

And there the matter sat until the copies of Marine Corps Times started disappearing from the front of exchange stores this past December.

Though there are differences between my earlier adventures with an X-Acto knife and a photo caption—my newspaper was owned and controlled by the military chain of command, whereas Marine Corps Times operates independently (and, to the best of my knowledge, has never called the commandant “Jimmy”)—it essentially boils down to the same thing: an angry high-ranking official, facing perceived embarrassment, makes a power play to stifle the release of information.

The relationship between the military and the Fourth Estate has been strained for decades, with the first threads starting to fray and unravel during the Vietnam War. As public affairs specialists, my colleagues and I spent the better part of our careers trying to convince military commanders that reporters with tape recorders were not the enemy. Sure, some generals (the savvy ones) can be very media-friendly; but I’ve known plenty who rapidly duck out of sight when a TV news truck shows up. These are the officers who have yet to learn that success on the battlefield does not mean their power can be equally wielded over the civilian news media.

But this is not the New York Times we’re talking about here; it’s the Marine Corps Times. While editorially it has the freedom to take the Corps to task, it’s also by its nature sympathetic to issues facing service members and remains a popular, trusted source for news about career progression, policy changes, and pay and benefits. By trying to “punish” the paper, it seems noses are being cut off not just to spite, but to save, faces.

Military officials have tried to downplay the connection between Marine Corps Times’ investigation into Amos’ actions and the newspaper’s vanishing act in exchange stores. According to a statement made by Maj. Shawn Haney, spokeswoman for Manpower & Reserve Affairs, the decision to move Marine Corps Times away from customers was all part of an effort to “professionalize the front areas of our stores.”

It continued: “As a result, the store entry merchandising strategy was reviewed and new directives were issued on how and where publications are to be displayed.”

Apparently, however, the Marine Corps Times wasn’t the sole focus of this new strategy. “Our review was conducted on all publications, not one single publication,” Haney said in an e-mail.

Exchange managers were told to move the newspapers to make room for the commandant’s reading list and that of the “First Lady of the Marine Corps,” Amos’ wife Bonnie.

deGrandpre attempted to resolve the issue privately—“on a business level," he said—for six weeks, hoping to negotiate a return to the checkout stands. “No one would meet with us and we kept getting rebuffed, so we decided to go public with it.”

In a Feb. 9 story published online, Marine Corps Times questioned its abrupt relocation and hinted that it smacked of censorship. In that article, the newspaper quoted an anonymous source with insider knowledge about the relocation directive who said, “It is no secret [in the Pentagon] that the commandant does not like Marine Corps Times.”

Three days later, after two months of empty racks and amid growing criticism from Marines and other media outlets, Amos himself ordered the newspaper be returned to the front of stores. In a statement released on the service’s official Facebook page, Gen. John Paxton Jr., assistant commandant of the Marine Corps, wrote: “Reaction to the Marine Corps Times’ relocation demonstrated a clear misunderstanding of intent.”

That intent, on the part of the Marine Corps, seems to be tied to Amos’ “Reawakening” campaign, launched last Fall. The commandant toured installations and circulated a video in which he announced a desire to reinforce Corps standards and discipline in barracks life and to crack down on discipline issues such as drunken driving, hazing and sexual assault. Re-evaluating the placement of products in exchanges is just one aspect of this holistic approach to strengthening values.

“I never thought we would be part of those problems,” deGrandpre said.

On Feb. 26, Amos took a defensive position on social media, releasing this statement on the Marines' Facebook page: "There was never any intention to ban the Marine Corps Times from the [Post Exchange]--period, none. I'm probably not the first commandant that's been frustrated with the way the Marine Corps Times handles information and how they put it out and how they write their stories, and I'm probably not going to be the last, but I want to be clear to all Marines, there was never any intent nor will the Marine Corps Times be banned from the Marine Corps exchanges."

For now, Marine Corps Times has reclaimed its place near the cash registers, but that might be temporary. “It’s pending completion of a comprehensive review involving focus groups,” deGrandpre said. “It’s unclear how long that will take or who’s involved.”

Nonetheless, he added, “I count this as a victory for the notion of free press.”

Editors note: This story was updated to include a statement from General Amos addressing his relationship with the Marine Corps Times, that was released after the article was originally posted.