Players armed with high-priced lawyers and publicists, and backed by a players’ union led by a former prosecutor, have mined sometimes arcane labor law to argue they were denied due process and to resist Goodell’s self-proclaimed goals to rein in misconduct.

“It really is exceptional how the federal courts have taken on the role of super-arbitrator of the N.F.L.’s disciplinary standards,” said Michael LeRoy, a sports labor law specialist at the University of Illinois, Urbana-Champaign. “Commissioners have traditionally been godlike authorities dating back to Judge Kenesaw Mountain Landis. The fact that you can go to court and get a judge to tell the commissioner what he can and can’t do is extraordinary. It feels there are three parties at the bargaining table: the N.F.L., the union and the courts.”

The Brady case is emerging as the most vivid example of Goodell’s efforts and their pitfalls.

In vacating Brady’s suspension, handed down in May after a league investigative report determined the quarterback was most likely aware that two team equipment staff members had deflated balls in an apparent bid to give him a better grip on them, Judge Richard M. Berman of Federal District Court in Manhattan did not focus on whether Brady had tampered with the game balls. He did not question the outcome of the game, a 45-7 Patriots victory over the Indianapolis Colts as the team marched on to win the Super Bowl.

Instead, he focused on the narrower question of whether the collective bargaining agreement between the N.F.L. and the players’ union gave Goodell the authority to carry out the suspension, and whether Brady was treated fairly during his attempt to overturn the punishment.