The National Football League beat Tom Brady in the Deflategate saga Friday afternoon, when Brady announced on his Facebook page he would cease his legal fight. After 545 bizarre days, the NFL got Brady to retreat into a four-game suspension and reinforced its total authority in player discipline. That doesn’t mean the NFL won, though. Over more than 17 months fighting Brady, the NFL maintained its power but utterly lost track of why that power mattered.

The real issue behind Deflategate traces back to about 2007, shortly after Roger Goodell assumed the NFL commissioner’s office. After a spate of arrests and off-field problems gave the league a public-image black eye, Goodell wanted to strengthen his ability to suspend troublemakers. Fans called for stiffer punishment, and even players agreed. The NFL wanted to protect its reputation. Players believed a small cluster of misbehaving players had given them an unfair, inaccurate portrayal.

“We were all fed up,” said one former player who worked closely with the NFL Players Association. “When we trusted Goodell, that’s when our first mistake was made. We wanted to clean the game up and wanted to send the message that those bad apples didn’t define us. We were all on board with trying to come down on guys like that. I think that was opening the door to people beginning to believe the players [union] would allow players to be over-punished.”

The sides agreed to give the league more power to discipline players for off-field incidents other than substance abuse and gave the commissioner “full authority to impose discipline as warranted.” In April 2007, Adam “Pacman” Jones received a season-long suspension owing to a series of arrests related to drugs and violence, mostly occurring at strip clubs. The NFLPA, led by Gene Upshaw and Troy Vincent at the time, supported the policy.

It was, at the time, the public-relations victory the league wanted. The lesson the NFL took from the episode should have been that it can affect change by cooperating with the union. Instead, it took a simpler lesson: that it can solve public-relations issues best by asserting control. That’s what the league’s power was all about – trying to make sure it would look good to fans.

Players started to complain about what they viewed as arbitrary punishment for on-field offenses. The Saints’ bounty scandal from 2011, when Goodell’s initial penalties were overturned on appeal by former Commissioner Paul Tagliabue, further showed the danger of the NFL holding full control of the disciplinary process.

The league clung tight to its power in 2011 collective bargaining talks, after owners locked out the players. The NFLPA side was unwilling to make concessions in order to weaken Goodell’s authority. Its priorities were player safety, revenue split and the rookie pay scale. The players didn’t like Article 46, the language that gave Goodell such broad powers, but they didn’t care strongly enough to compromise on other issues, such as an 18-game schedule. They figured, not irrationally, that off-field discipline would apply to a minute percentage of players, anyway.

And so Article 46 stuck. Goodell fought Brady and the NFLPA tooth-and-nail over the past 15 months, not so much because the league cared deeply about Brady sitting for four games on the New England Patriots’ bench. The league wanted to protect its power, and through legal channels and a byzantine, endless appeals process, it did.

At what cost? The NFL has preserved its power, but in doing it has compromised the fan support it sought to win by acquiring that power in the first place. The league lost sight of the reason – public confidence – why it so badly wanted authority to discipline players in the first place. Fans and players loathe Goodell and reflexively distrust the league when disciplinary matters arise. It’s the precise result the league intended to avoid when it acquired disciplinary control.

Power for the sake power is pointless. The NFL forgot that. Years ago, the public and even players wanted the NFL to be harsher in how it disciplined players. The NFL acquired and abused that power, to preposterous degrees in Brady’s case, a matter of air inside a football. The public it wanted to appease years ago now views it as heavy-handed and incompetent.

The case isn’t over yet. The NFLPA said it will reserve its right to take Brady’s case to the Supreme Court in order to challenge’s Goodell’s authority. The union has good reason to attempt to take its case to the Supreme Court, and not just for the ostensible cause of challenging Goodell’s authority on behalf of all players.

Deflategate turned the NFL’s disciplinary power into a major issue for the next collective bargaining session. If the current outcome holds, the NFL can use Article 46 as a cudgel to increase its share of revenue. If the union wants to limit the NFL’s power, and surely it will be under pressure to do so, then it will have to trade something in negotiations. That something, in some form, will be money.

It’s odious for the NFL to use its power in such a way. No matter how many fans know it and agree, what will it matter? Is it going to stop anybody from ordering Sunday Ticket? Or skipping their fantasy draft? Or buying a personal seat license? No matter what fans think about the league, they are addicted to the product. Even the NFL can’t screw up the games.

Maybe it did win, after all. The NFL, no matter how little it deserves it, always wins in the end.