The NFL got tough with the New Orleans Saints when it was found they levied bounties on opposing quarterbacks, but the league didn’t like the Saints, who spent their Super Bowl week high-hatting the highest-hatted league in the world.

The NFL sought to get tough, albeit in belated fashion, with Ray Rice after the video of his elevator knockout surfaced, and then with Adrian Peterson, indicted for child abuse as the tempest regarding Rice was raging. (In typical Roger Goodell style, the commissioner overreached; suspensions of Rice and Peterson were overturned.)

The blustering NFL has now been backed into a corner. It was easy to come down on a rogue organization and to take a stand against domestic violence. (Nobody can defend domestic violence.) But what will the Tiffany League do after an investigation found it “probable” that its highest-profile franchise “was involved in a deliberate attempt to circumvent the rules.” Will the league that got righteously indignant with Sean Payton and Ray Rice treat the golden boy Tom Brady the same way?

The biggest loser of the 243-page report issued Wednesday by attorney Ted Wells wasn’t Jim McNally, the officials’ locker-room attendant at Gillette Stadium, or Patriots equipment assistant John Jastremski. The biggest loser was the quarterback who has won four Super Bowls, the fourth coming two weeks after he threw footballs that Wells’ investigation found weren’t up to NFL snuff.

From the report: “Brady denied any knowledge of or involvement in any efforts to deflate game balls after the pregame inspection by the game officials. He claimed that prior to the events surrounding the AFC championship game, he did not know McNally’s name or anything about McNally’s game-day responsibilities, including whether McNally had any role relating to game balls or the game officials. We found these claims not plausible and contradicted by other evidence.”

Got that? The Wells Report called Tom Brady a liar. Bill Belichick is given a pass, but his quarterback is singled out for his stonewalling. From the report: “Brady’s refusal to provide us with his own emails, text messages and phone records … limited the evidence available for our review and analysis.”

Other sources proved more availing. Jastremski’s phone records show that, in the three days after the AFC Championship game, the famous quarterback had six early-morning conversations with the assistant equipment man totaling 55 minutes and 51 seconds. (“You good Jonny boy?” Brady texted Jastremski, proving that even superstars dispense with commas.) Apparently Brady was so consumed by Deflategate that he wanted to get everyone’s story straight.

The story Wells wound up getting: That McNally “removed the game balls from the officials’ locker room … McNally entered (a) bathroom with the game balls, locked the door, and remained in the bathroom with the game balls for approximately one minute and 40 seconds. He then left the bathroom and took the bags of game balls to the field.”

Further note: In a May 2014 text to Jastremski, McNally described himself as “the deflator.” Barely a week before the AFC title game, McNally was given a game jersey and two footballs autographed by the Brady who claimed he didn’t know who McNally was.

The Patriots’ first Super Bowl victory has long been the subject of rumors that the Rams’ Saturday walk-through was videotaped. (Goodell found no evidence of this, though he found proof of other taping.) Title No. 4 has now been thrown into question. (Owner Robert Kraft, sometimes described as the NFL’s deputy commissioner, issued a statement saying he was “disappointed” in the investigation, which he labeled “incomprehensible.”)

The matter of discipline officially falls to Troy Vincent, the vice president of football operations, but the matter will again become a referendum on Goodell. The commissioner attended a party at Kraft’s home the night before the game in question. If the commissioner’s league doesn’t suspend Kraft’s starting quarterback for at least a month, we’ll know who really runs the NFL.