Whether they’re college football fans or not, many Americans are aware of the NCAA’s two-year-plus investigation into the University of Miami’s football and basketball program. After all, the story had all the ingredients to captivate the general public.

In 2011, a major news outlet broke the story not only alleging that athletes took money and free drinks from a booster, but the same booster in question was a convicted felon in jail for a $930 million Ponzi scheme and purportedly paid for abortions on behalf of players (an unproven accusation).

But as the NCAA investigation came to a close on October 22, the biggest loser was not the school who was accused of wrongdoing and received resulting penalties, but the NCAA itself. Do you think if the NCAA knew the outcome two years ago it would have taken the word of a criminal and dug in to “bury” the University of Miami?

The NCAA made a calculated risk to use this case as an avenue to reclaim control of major college athletics and the big business it has become, and instead lost its reputation in the process. (This UCLA case and the Ed O’Bannon/video game lawsuit haven’t helped either).

Over the past two years, the NCAA has eroded its brand equity by not only failing to properly handle the UM investigation from an operations standpoint – after all, nine investigators were either fired or suspended during the inquiry – but also by continually failing to take public accountability and control the narrative of this story.

The expectation of law and order (or at least in the NCAA’s case bylaws and governance) is that justice is carried out fairly. However, when the judge, jury and executioner are all “out of order,” the mob will revolt. And the mob’s victim is the trampled reputation of the NCAA.

When you are an amateur athletics organization overseeing a multi-billion dollar business, maintaining your core message of amateurism surely is difficult. However, while these waters might be tough to navigate, it is still important to remember that upholding a positive public perception is your best defense. This is where they NCAA failed.

What the NCAA can do to fix their reputation is a bigger question for another time. (I think blowing up the system and rebuilding it will have to be the start.) In the meantime, there is an important lesson for PR professionals here.

Reputation management requires action and communications that are true to the organization and its audience. It is an ongoing process and not something that can be initiated once faced with a problem. Because once the damage is done, it might be a long time before the organization is “winning” once again.