As expected, New England Patriots quarterback Tom Brady formally appealed the four game suspension imposed by the National Football League over the so-called “DeflateGate” scandal, and N.F.L. Commissioner Roger Goodell said he would personally hear the appeal rather than handing it off to an outside arbitrator:

Tom Brady formally appealed his four-game suspension on Thursday for his reported role in the deflation of footballs before the A.F.C. championship game in January against the Indianapolis Colts.

Commissioner Roger Goodell said Thursday night that he would hear the appeal.

“Commissioner Goodell will hear the appeal of Tom Brady’s suspension in accordance with the process agreed upon with the N.F.L. Players Association in the 2011 collective bargaining agreement,” Greg Aiello, an N.F.L. spokesman, told The Associated Press.

Citing previous overturned punishments, the players’ union had urged Goodell to appoint a neutral party to hear the appeal.

“Given the N.F.L.’s history of inconsistency and arbitrary decisions in disciplinary matters, it is only fair that a neutral arbitrator hear this appeal,” the union said in a statement.

If the league and its investigators are truly confident in its case, the union said, “they should be confident enough to present their case before someone who is truly independent.”

The appeal must be heard within 10 days.

Brady also hired Jeffrey L. Kessler, an antitrust lawyer, to help in his defense.

Kessler has worked successfully on behalf of athletes in several cases involving the N.F.L., the N.B.A. and the N.C.A.A.

Under league rules, Goodell is the default arbitrator in cases such as this. However, as noted, in the recent past he has handed off some of the league’s more controversial high profile suspensions to outside arbitrators, most notably his decision to impose a lifetime ban on Ray Rice last September after having initially only suspending him for two games and the suspension imposed on Adrian Peterson after he was plead guilty to misdomeanor child abuse. Ultimately, Rice won his appeal while Peterson’s suspension was upheld. In this case, while Goodell was apparently not involved in the investigation or the penalties that were imposed earlier this week, Brady and the NLFPA obviously feel that he would be biased in favor of the league. Their options after Goodell’s announcement are unclear, although it is possible that there could be litigation if the appeal does not result in the elimination or reduction of Brady’s suspension.

Meanwhile, earlier in the day yesterday, the Patriots released their own rebuttal to the Wells report:

So it has come to this. After four months of speculation and outrage, as well as an investigation costing millions of dollars and diverting attention from what would seem to be more serious matters, the focus of the N.F.L.’s air-pressure scandal has seemingly narrowed to one man — a crass, overweight jokester with a full bladder.

This was the latest contention of the New England Patriots, who said in a report issued Thursday that Jim McNally, a part-time equipment manager, referred to himself as the “deflator” only to indicate his desire to lose weight.

The Patriots’ rebuttal to the investigative report compiled by Theodore V. Wells Jr. also said that McNally used a private bathroom at Gillette Stadium before the A.F.C. championship game for one minute and 40 seconds not to take air out of footballs, as the Wells report suggests, but to relieve himself. The Patriots’ rebuttal argues that 100 seconds is the length of time consistent for “a gentleman to enter a bathroom, relieve himself, wash his hands, and leave.”

From the Patriots’ standpoint, the science is indisputable. So is the fact that with each passing day it becomes harder to take the matter seriously.

This whole affair first veered toward farce before the Super Bowl, when Patriots Coach Bill Belichick said in a news conference that he was not theMona Lisa Vito of air pressure in footballs. The saga has now slipped further, to the point that the most important issue now facing the N.F.L. would seem to be why a middle-aged employee chose to enter a bathroom — and not painful allegations that the league overlooks domestic violence, drug use and the long-term physical effects of the game.

Based on conclusions drawn in Wells’s investigation, the N.F.L. suspended Tom Brady, for four games. Brady on Thursday appealed the suspension, which will be heard by Commissioner Roger Goodell.

Brady was not shown to have deflated the footballs or orchestrated the deed, but to have been “generally aware” that McNally had “probably” deflated the balls in the bathroom. The report also noted that Brady refused to hand over his cellphone to Wells, a private citizen, for the investigation.

The Patriots countered that Brady withheld his phone on behalf of the rights of all future players who could face an investigation by the N.F.L., which has been accused of heavy-handed tactics in the past.

The Patriots’ rebuttal, which sets the team on a course directly at odds with the league, mirrored the Wells report in one way, by diminishing the impact of its arguments by including some questionable claims — most notably the deflator weight-loss argument, which only invites ridicule.

Written by the team’s lawyers, the Patriots’ rebuttal suggested that Wells led witnesses to answers that supported his conclusions, a claim certain to anger an already aggrieved Wells. On Wednesday, Wells went on a league-sponsored conference call and strenuously defended his report while dismissing questions about how much money the league paid him to produce it.

You can read the full Patriots rebuttal for yourself and draw your own conclusions. At the very least, this kind of combative attitude seems to indicate fairly clearly that this dispute is unlikely to end with just appeals decided by Roger Goodell.