New England Patriots owner Robert Kraft, coach Bill Belichick and quarterback Tom Brady have had significant disagreements this season — behind closed doors — that have led to dysfunction and threaten to end an owner-coach-quarterback relationship that helped the franchise win five Super Bowls over the last 17 years, according to an ESPN report citing a dozen New England staffers, executives, players and other league sources.

Much of the friction stemmed from Brady's trainer, body coach and business partner Alex Guerrero, who helped Brady promote a training method both in his new book, "The TB12 Method," and within the team.

The TB12 Method had a controversial philosophy on injury-recovery mindset and was loaded with so many rules that one unnamed Patriots staffer said in the ESPN report it "felt like a cult."

Guerrero, invited on the Patriots' staff as a consultant, would blame Patriots trainers for injuries.

Belichick confronted Brady in early September about pressure that players were feeling by Guerrero to train at TB12 instead of with the team.

There was no resolution to the meeting, ESPN reported. Belichick, in an effort to clarify Guerrero's role, later emailed Guerrero to let him know he wasn't permitted access to the team headquarters because he wasn't an employee.

Among the key disagreements among the three franchise leaders was who would be around last, as well as management of past controversies.

Brady, according to the ESPN report, wanted backup QB Jimmy Garoppolo gone.

The Patriots eventually dealt Garoppolo to the San Francisco 49ers.

The trade left Belichick feeling "furious and demoralized," while Brady's body language showed a "liberated" resolve.

That outcome, a Patriots staffer told ESPN, showed Brady "won."

The story adds that in the midst of the internal dysfunction, Belichick has "become good friends" with NFL commissioner Roger Goodell, meeting with him for a long and private meeting earlier this season.

Another claim: Kraft, according to the report, privately told associates that he went too far in his attacks against the NFL during the Deflategate scandal and penalty, but he was forced to support Brady "for the fans."

Messages left by USA TODAY Sports to the Patriots on Friday morning were not immediately returned.

The team denied dysfunction in the ESPN story and cited “several inaccuracies.”