FOXBOROUGH, Mass. — The NFL was determined to blame Patriots quarterback Tom Brady for deflated footballs in the AFC title game, and the investigation omitted key facts and buried others, Brady’s agent said Thursday.

Don Yee said the report prepared by NFL-appointed investigator Ted Wells was “a significant and terrible disappointment.”

The 243-page report found that two Patriots employees violated rules covering game balls, and that Brady was “at least generally aware” of the plans to doctor the footballs to his liking. The report found some of Brady’s claims were “implausible,” adding: “It is unlikely that an equipment assistant and a locker room attendant would deflate game balls without Brady’s knowledge and approval.”

Yee said the report “reached a conclusion first, and then determined so-called facts later,” and said Wells’ firm makes a lot of money from the NFL and put out a report that benefits the league.

Yee didn’t elaborate on how blaming the NFL’s biggest star for the embarrassing story that dominated the news in the run-up to the Super Bowl helped the league.

The Patriots defeated the Seahawks in the Super Bowl, and Brady was the MVP.

Yee emphasized that the league should not have allowed a sting in a playoff game.

“What does it say about the league office’s protocols and ethics when it allows one team to tip it off to an issue prior to a championship game, and no league officials or game officials notified the Patriots of the same issue prior to the game?” Yee said. “This suggests it may be more probable than not that the league cooperated with the Colts in perpetrating a sting operation.”

Yee also said the investigators didn’t understand football and left out key parts of Brady’s testimony.

“It is a sad day for the league as it has abdicated the resolution of football-specific issues to people who don’t understand the context or culture of the sport,” said Yee, who was present for Brady’s interview.

Brady has been able to shrug off previous controversies: The “Tuck Rule” non-fumble, the Patriots’ illegal videotaping, his name popping up in baseball’s steroid investigation, an out-of-wedlock child with the actress he jilted before marrying the world’s richest supermodel.

But the deflated footballs investigation might do what none of the other controversies and near-misses could: tarnish the legacy of a four-time Super Bowl champion.

“What I see is that he goes from being ‘Tom Perfect’ to ‘Tom Not-So-Perfect’ in some people’s eyes,” Marc Ganis, president of sports business consulting firm SportsCorp, said Wednesday.

The findings were forwarded to the league’s disciplinary chief for potential punishment. Brady could be fined or face a suspension that would keep him out of Week 1 — the marquee league opener at which the Super Bowl banner would traditionally be raised.

The Patriots did not respond to a request for a comment from Brady or coach Bill Belichick, who was exonerated in the report. The team canceled a previously scheduled availability for Thursday.

Brady was scheduled to appear at a Q&A at Salem State University Thursday night.

Owner Bob Kraft issued a spirited statement in defense of his team and questioned Wells’ conclusions. “To say we are disappointed in its findings, which do not include any incontrovertible or hard evidence of deliberate deflation of footballs at the AFC Championship Game, would be a gross understatement,” he said.

But Wells concluded there was no plausible explanation for the deflated footballs except deliberate tampering. And text messages to and about Brady led the investigator to conclude that he was aware, if not more actively involved, in the scheme.

Regardless of his punishment, Brady’s legacy is now tied to the scandal. But the main effect of that, Ganis said, could be to solidify opinions that are already largely entrenched: Opposing fans will continue to doubt him, and fans in New England, where he was once seen as a candidate for the U.S. Senate, will rally to his defense.

“As far as his marketability goes, he is still arguably the most marketable player in the NFL,” said Ganis, who grew up a New York Jets fans and is now based in Chicago.

“Tom Brady has been the face of the NFL, with Peyton Manning, for a number of years. He has been an extraordinary ambassador, with cross-over popularity,” he said. “If this is all there is, it will be something that is talked about him when he is elected to the Hall of Fame.”