Robert Kraft has often had Roger Goodell's back. AJ Mast/AP Despite one of the ugliest seasons in NFL history thanks to a number of issues and how the league handled them, commissioner Roger Goodell has repeatedly said he has no intention of resigning.

However, Goodell's biggest supporter, New England Patriots owner Robert Kraft, is suddenly singing a different tune and the commissioner's job may no longer be secure.

In a recent story for GQ magazine, titled "The Season from Hell: Inside Roger Goodell's Ruthless Football Machine," Gabriel Sherman outlines just how close Goodell and Kraft have been and how it was Kraft that backed Goodell during the uproar over how the league handled the Ray Rice domestic assault scandal.

According to the story, when the Rice case began to spin out of control, it was Kraft who arranged for Goodell to do his first on-air interview, on CBS with a woman as the interviewer. It was also Kraft who lobbied other owners to publicly support Goodell.

Goodell and Kraft were so close, at least one NFL executive refers to Kraft as "the assistant commissioner."

Kraft was also the owner who "vigorously defended" Goodell's $44 million salary.

The relationship between Kraft and Goodell was further cemented in the public eye when the two were photographed together at a party just days prior to the AFC Championship game. This led Richard Sherman of the Seattle Seahawks to speculate that the league won't punish the Patriots over Deflategate because of the conflict-of-interest.

But then the league discovered that the Patriots used deflated footballs during the AFC Championship game, possibly inaccurate information was leaked to the press, and the relationship appears to have turned sour since.

There have been several recent incidents, some more telling than others, that when taken on their own can be easily explained away. But when the incidents are viewed as a whole, they suggest that Goodell has lost his most important ally.

Here is a rundown Kraft's recent actions:

Mike Reiss, who covers the Patriots for ESPN.com and whom Peter King of SI.com calls "well-plugged-in," recently wrote that it appears that the relationship between Goodell and Kraft "is not in a good place" and the biggest issue is the leaks that came from Goodell's office.

"My sense is that Kraft feels stung by Goodell, who he had backed in the wake of the mishandled Ray Rice domestic violence case," Reiss wrote for ESPN.com. "The longstanding relationship between the two is not in a good place based on the league’s handling of the team’s under-inflated footballs and specifically public leaks. For perhaps the first time, I sense Kraft is doubting Goodell’s leadership, and if Goodell loses one of his top supporters I wonder how much it could threaten his hold on the job."

Reiss does acknowledge that this could just be something that needs time to "smooth itself over." However, at the very least, the relationship between Goodell and one of his strongest supporters suddenly appears to be strained.