From the Ray Rice scandal to DeflateGate, NFL Commissioner Roger Goodell has dealt with a lot of scrutiny this season. (John Raoux/Associated Press)

The NFL season is ending, just as it began, in turmoil.

As Super Bowl week arrives, the question was to be: Has the NFL weathered the storm? After the league, and Commissioner Roger Goodell in particular, were heavily criticized in September amid a public outcry about how the sport reacted to the criminal charges faced by prominent players Ray Rice, Adrian Peterson and Greg Hardy, the NFL temporarily managed to return the focus to the games themselves.

But the turbulence returned last week with the burgeoning controversy over the revelation that the New England Patriots used under-inflated footballs during their lopsided victory over the Indianapolis Colts in the AFC championship game.

The latest scandal involving the Patriots has reignited the debate, with great ferocity, as to whether the franchise’s winning legacy has been tarnished by episodes such as Spygate and now Deflate-gate that have led detractors to label the team cheaters. Supporters have contended that the Patriots have been accused falsely and targeted unfairly because of their success.

The incident also has put the NFL back in a prominent place on the network newscasts and in the national conversation for something other than the otherwise-glittery Super Bowl matchup next Sunday in Arizona between the Patriots and Seattle Seahawks. Some within the sport acknowledge they worry that the mounting issues might be eroding the public’s trust in the sport and its leaders.

“Without a doubt,” said Eric Winston, the veteran offensive tackle who is the president of the NFL Players Association. “I think the way things have been handled has turned off the public, turned off the fans. I see it on Twitter. I hear it from people just walking around. It’s too bad. It doesn’t have to be that way.

“It’s not only the league office,” Winston said. “It’s the owners. When are they going to step in and do something to make sure things are handled in the right way? It’s easy to look at the bottom line and say everything is fine. But you never see the iceberg until you hit it, right?”

The seriousness of what the NFL is confronting in the Patriots matter seems insignificant compared to the gravity of the issues arising from the Rice, Peterson and Hardy cases.

The Rice case put domestic violence in a more prominent place in the national consciousness after TMZ released in September violent images taken from inside the Atlantic City hotel elevator in which Rice struck Janay Palmer, then his fiancée and now his wife, in February.

Peterson reached a plea agreement in a case arising from allegations that he struck his 4-year-old son with a switch as a disciplinary measure. Hardy awaits a jury trial after being found guilty by a judge of assaulting and threatening his former girlfriend.

The proliferation of double-entendre comments and headlines in the Patriots case perhaps contributes to a notion that the subject matter is whimsical and insignificant. But the back-and-forth among fans and other observers over the team’s reputation has been highly charged. And within the context of the integrity of the sport, the Patriots’ use of footballs that were not within NFL specifications is meaningful, many onlookers say.

Even Patriots quarterback Tom Brady, while being questioned during a news conference Thursday about his role in the incident, said: “It’s very serious. This is a very serious topic. Obviously the integrity of the sport is very important.”

Brady also said: “I think that’s a very important issue to always be mindful of as an athlete. … I think we set a great example for the younger athletes, the younger kids, the college kids, the high school kids. We want to be the ones to set the great example.”

Peter Schaffer, a veteran agent whose clients include NFL players, coaches and front office executives, said the responsibility ultimately rests with Goodell and other league leaders.

“Every situation we’ve had has come from the fact that the league has reacted to things and has not been proactive to solve a problem before it happens,” Schaffer said. “When Paul Tagliabue was the commissioner, people said, ‘He’s not doing much.’ He’s still not even in the Hall of Fame. But people did not give him enough credit for steering the ship straight through calm waters. He solved problems before they arose and he avoided them.”

Schaffer said that the Goodell-led NFL, in his view, has focused too intently on disciplinary actions rather than common-sense preventative measures.

“This thing that’s happening now — why would you let teams be in control of their own footballs? It doesn’t make any sense,” Schaffer said in a telephone interview. “And if the NFL had been proactive about domestic violence years ago, you wouldn’t have seen the same thing that happened earlier in the season. They’ve been leading through discipline. It needs to be through education and awareness. Everything that’s been put in place this year—why did we need these events for this to happen? Every problem that we had this year was easily solved if we had leaders who were forward-thinking.”

The NFL acknowledged Friday that the footballs supplied and used by the Patriots on offense in the first half of their 45-7 victory over the Colts were under-inflated and did not meet league specifications. The league said its investigation has not determined whether that was done deliberately by the Patriots.

On Saturday, Patriots Coach Bill Belichick said at a hastily called news conference he was certain that the team had not broken any NFL rules. Belichick also staunchly defended the team’s honor and integrity.

The issue has been extremely polarizing, but some are doing their best to remain calm and take a wait-and-see approach.

“That’s still ongoing,” Winston said in a phone interview late last week. “It’s hard to tell. That process has to play out. It’s easy to jump to conclusions.”

The NFL continued to prosper this season as a business entity. Regular season games averaged 17.6 million television viewers per broadcast; that was the second-most in NFL history to the 17.9 million viewers per game in the 2010 season, according to the league. An NFL game was the most-watched show on TV during each week of the regular season. The NFC championship game between the Seahawks and the Green Bay Packers was the most-watched program on television since the last Super Bowl with an average of 49.8 million viewers, and had a peak of 60.5 million viewers as the game entered overtime.

The NFL extended its deal with DirecTV for $1.5 billion per season, up from $1 billion annually in rights fees under the contract that was to expire following this season. The Buffalo Bills, located in one of the league’s smallest markets, were sold for $1.4 billion by the Ralph Wilson estate to Terry and Kim Pegula.

Yet even as the money continued to flow into the sport’s coffers, the relationship between the league and the players’ union remained contentious. They were at odds at practically every step in the Rice and Peterson cases. The union filed a grievance last week over the NFL’s enactment of a reworked personal conduct policy in December.

“We’ve had plenty of talks — some public, some not,” Winston said. “I don’t know that the dialogue is lacking. It’s the want-to. Until we decide — until they decide, the owners decide — we all want to work together and get this done and get it done the right way, it’s just going to be this constant turmoil.”

This could be a time for the NFL to bask in a glorious matchup between the Patriots, seeking their fourth Super Bowl triumph with Belichick and Brady in charge, and the Seahawks, coming off a dominant victory over the Denver Broncos in last year’s big game and arriving in Arizona fresh from a memorable and improbable comeback against the Packers.

Instead, the NFL just has launched another investigation and Super Bowl week will be filled with talk of deflated footballs, pounds per square inch and possibly tainted legacies.

“I think it’s disappointing that a situation like this happens,” Brady said Thursday. “Obviously I’d love to be up here talking about [the Super Bowl] in a very joyful mood. These are the two best weeks of the year if you happen to be one of the two teams still playing. So … it should be a great two weeks. I’m obviously very disappointed that we have to be having a press conference like this. I wish I could give you more answers or the answers that you guys were looking for. But I don’t have some of those answers.”