Despite how this whole thing started, the court’s ruling was not actually about deflated footballs.

A federal judge says quarterback Tom Brady of the New England Patriots can play, after all. The court ruled to reverse the star quarterback’s four-game suspension following the controversy over under-inflated footballs in last season’s AFC championship.

“It’s a case about deflated procedures, I think,” says law professor Roger Abrams of Northeastern.

“The court was almost angry at the National Football League for the way they treated Tom Brady.”

Brady’s four-game suspension followed the publication of the so-called Wells report, which detailed the investigation into the alleged scheme to deflate footballs.

“The Commissioner made much of the fact that Ted Wells’ investigation was independent, when in fact, at least to me it seemed like the work of a very good lawyer supplying information to his client, rather than independent.”

The federal judge’s ruling says Brady wasn’t given a fair chance to challenge that independence. After NFL Commissioner Roger Goodell appointed himself to be the arbiter in the case, rather than someone more independent, he denied a request by Brady’s union, the Players’ Association, to see investigative files like notes from witness interviews. And, Abrams points out, Goodell didn’t agree to testimony from NFL general counsel Jeff Pash, who served as a co-investigator in the case.

“What this really did was keep the Brady people from understanding the basis for the initial determination that he was generally aware of certain violation of rules. Pash could have helped considerably.”

Also, the judge said the NFL didn’t tell Brady what punishments he could face for his actions. Alfred Yen is a law professor at Boston College.

“Never was he told that he could be suspended for being involved with deflating footballs or being aware of football deflation. Nor did they tell him he could be suspended for failing to cooperate fully with an NFL investigation.”

Also, the judge said Brady wasn’t told in advance that the discipline for his actions would be equal to the punishment for a player using performance-enhancing drugs – four games on the bench.

Yen says the NFL has itself to blame for losing this case.

“I think the Commissioner made a significant miscalculation by deciding not to settle the case when he had an opportunity to do so. He gave the judge the opportunity to nitpick what he had done.”

And, he says, that’s an invitation to other players to nitpick future decisions by the commissioner. Yen points out this isn’t the first disciplinary ruling by Goodell to be reversed by courts. Punishments have been overturned in recent years for Adrian Peterson and Ray Rice, as well as members of the New Orleans saints for a pay-to-injure program that became known as bounty-gate.

The NFL says it plans to appeal the judge’s decision. And Labor lawyer Peter Moser of the firm Hirsch, Roberts Weinstein won’t say how he thinks that will turn out.

“You know, I’ve given up making predictions as to what’s going to happen in cases like this. Because folks like me initially thought that Judge Berman was probably, sort of reluctantly, going to uphold the NFL’s decision.”

Moser says the lesson for Goodell in the decision is perfectly clear.

“Why on Earth would you allow yourself to be appointed the arbitrator essentially over your own decision and to deny access to evidence and witnesses, when those are the very few standards that you can be overruled on on appeal.”

And he says regardless of how the NFL’s appeal of the new ruling goes, that’s a point they’ll probably keep in mind next time something like this happens.