We know how this controversy started. The Colts beat reporter Bob Kravitz tweeted out that the NFL is investigating whether the Patriots messed with game balls in the AFC Championship. Despite the controversy surrounding them, the Patriots were able to prevail in Super Bowl XLIX over the Seattle Seahawks, 28-24. Hundreds of media leaks and a report written by Ted Wells and Jeff Pash later, the NFL ended up suspending Tom Brady 4 games while fining the Patriots $1M along with confiscating a 2016 1st round pick and 2017 4th round pick. Tom Brady responded by hiring Jeff Kessler and appealed his suspension. The NFL ended upholding the suspension on the grounds of Brady "destroying" his phone. Brady has since taken this to court, where the controversy has escalated and has put heat on the NFL.
The issue with the suspension has nothing to do with air pressure anymore. Brady, Kessler, and the PA is suing over the process that led to the suspension and if it violated the Collective Bargaining Agreement. The main two cases that Kessler will have are about Troy Vincent and the "Law of the Shop". If Troy Vincent issued the punishment, that's a clear violation of the CBA. That's probably not the case because even Goodell is not that stupid. That means that the "Law of the Shop" is where Brady's camp has the best shot at overturning a suspension. When it comes to messing with footballs, the penalty is a $25,000 fine. When it comes to non-cooperation, the precedent set with the Brett Favre sexting case is a $50,000 fine. I don't think Brady was non-cooperative in the investigation, because Ted Wells did not initially ask for the phone.
The NFL wanted to have the appeal transcript sealed, but Judge Richard Berman would not have it. The appeal transcript, which Rich Hill summarized for you, reveals that the NFL realized they didn't have anything and made Tom Brady the scapegoat. Going the various sections of the transcript that Rich highlighted for us to read, it shows that the NFL was more concerned about punishing the Patriots and Brady instead of trying to find the truth. This changed the scandal from air pressure to a battle between the NFL and the PA over the Goodell's Judge, Jury, and Executioner power. If the suspension is allowed to stand, that could mean the NFL and Roger Goodell has free reign to arbitrarily discipline players without concrete evidence. The current CBA allows Goodell to be an arbitrator, despite the fact he represents the NFL Owners which disqualifies him from being an independent party.
Most of the NFL Owners probably don't care, but this scandal shows that Goodell is willing to drag down as many players as he can to stay in power. The owners have a lot of power over the players because the NFL career is very short compared to other sports with an average lifespan of 3.3 seasons and 5.5 for players that make an opening day roster their rookie year. With a short window to maximize their earnings for a sport that yields long term health problems, the players really can't afford to fight the NFL. However, Tom Brady does have the resources to fight the NFL and it's an opportunity for the PA to be able to set a precedent for the future. If the NFLPA succeeds in overturning the suspension in court, Goodell will not be able to set arbitrary and capricious punishments without them getting overturned in court. Courts have already overturned the Ray Rice and Adrian Peterson suspensions last year because both were Ex Post Facto suspensions following Goodell's policy changes to domestic violence in the 2014 season. The Brady case would give Goodell his 3rd strike and could be the first domino of Goodell losing his ability to be an arbitrator.
Goodell and Brady will be heading back to court later this month and perhaps there might be a settlement over the issue. I won't bank on it, although the released transcript really puts the NFL in a corner and puts Brady in a position of strength at the negotiating table. I'm not sure what will eventually happen, but we'll cross that bridge when we come to it.