By Kaitlan Collins and Kevin Liptak, CNN

(CNN) -- President Donald Trump was visibly distressed this weekend over the fallout that ensued from the story published in The Atlantic alleging that he privately disparaged the war dead.

In several conversations since the story was published Thursday, Trump vigorously denied that he made the comments and touted what he's done for the military. Two people who spoke with him said it was clearly a sign of how much the story had resonated with Trump -- and his fear that it could hurt his support with the military.

When the story first appeared on Thursday, Trump was outraged during his flight from Pennsylvania and demanded that aides begin denying it. That included sending his chief of staff Mark Meadows to the back of Air Force One to tell reporters it wasn't true. His angered reaction prompted officials to mobilize the massive pushback effort that began Thursday night.

By the weekend, however, Trump appeared more deflated than outraged at the allegations lobbed against him, based on conversations he had.

It was a relatively quiet weekend at the White House until Trump decided he wanted to hold a Labor Day news conference. Just as aides believed the story was quieting down, Trump accused top Pentagon military leaders of being beholden to defense contractors, an astonishing comment from the President as he's trying to bolster support with those people. Trump had been privately upset that more of the top brass at the Pentagon had not defended him in the wake of The Atlantic's story and some saw this as a response to that.

On Tuesday morning, Meadows claimed that Trump wasn't referencing Defense Secretary Mark Esper, a former top lobbyist for Raytheon, or the chairman of the Joint Chiefs of Staff, Mark Milley, when he made the comments -- though it's not clear who Trump would have been referencing instead.

"All the President is saying is that over the decades, some senior career politicians and Pentagon officials have shown an unwillingness to end our endless wars," a White House official told CNN. "This President stands with our soldiers serving on the front lines and our great generals and wants to responsibly end these conflicts to bring our troops home."

Trump's relationship with Esper has deteriorated significantly, and CNN has reported he will almost surely be replaced if Trump is re-elected.

It's also not clear how Trump's disparagement of the "military industrial complex" fits within his efforts to broker arms sales overseas -- a central element of his foreign policy -- including to countries like Saudi Arabia.

The White House has repeatedly pointed to on the record denials from aides such as Sarah Sanders and Zach Fuentes disputing the specific instance of what happened during Trump's November 2018 trip to Paris, one of the incidents outlined by The Atlantic.

But it has been obvious to some that denials from people who could stifle the story have not materialized, including the former chief of staff John Kelly or Joe Dunford, the chairman of the Joint Chiefs of Staff at the time. Kelly and Dunford traveled to the Aisne-Marne cemetery instead of Trump when his trip was canceled because of rain.