NFL referee Walt Anderson and Tom Brady during happier times in the AFC title game. Jim Rogash/Getty Images The NFL has concluded its months-long investigation into Deflategate and determined that it is "more probable than not" that two employees deliberately released air from game balls and that New England Patriots quarterback Tom Brady "was at least generally aware" of the plan.

The scandal, in which the Patriots were found to be using deflated game balls during their 45-7 victory over the Indianapolis Colts in the AFC title game, is a huge black eye for the Patriots and Brady, and it draws the legitimacy of last year's Super Bowl championship into question.

Perhaps the most dumbfounding part of this is that the NFL had more than one chance to stop it from happening and did nothing.

According to the report, the league first became aware of the possibility that the Patriots were deflating the footballs when Ryan Grigson, the general manager of the Colts, sent an email to two senior members of the NFL Football Operations Department days before the AFC championship game.

In the email, Grigson included a note from a Colts equipment manager that said the Patriots were known for deflating footballs. He added: "All the Indianapolis Colts want is a completely level playing field. Thank you for being vigilant stewards of that not only for us but for the shield and overall integrity of our game."

Here is the note from the equipment manager to the NFL. It describes exactly what NFL investigators believe happened before the AFC title game:

As far as the gameballs are concerned it is well known around the league that after the Patriots gameballs are checked by the officials and brought out for game usage the ballboys for the patriots will let out some air with a ball needle because their quarterback likes a smaller football so he can grip it better, it would be great if someone would be able to check the air in the game balls as the game goes on so that they don't get an illegal advantage.

That email was forwarded to several other league officials, including two senior members of the NFL Officiating Department, who responded by saying they would bring the issue up with Walt Anderson, the referee assigned to the AFC title game.

At no time was there any indication that the Patriots were made aware of the Colts' concerns or that the NFL was making members of the Patriots' front office aware of a potential rules infraction.

Mike Florio of ProFootballTalk.com spoke with an anonymous league official who said this would have never happened under previous commissioners.

"As one league source with no connection to the present controversy explained it to PFT in January, past Commissioners like Paul Tagliabue would have informed the Patriots of the situation," Florio wrote, adding that Tagliabue would have "warned them that the NFL is paying attention, that the league reserves the right to check the air pressure in the footballs during the game, and that any funny business would be met with a decidedly unfunny reaction from the league office."

Doing this would have almost certainly scared the Patriots enough to ensure that nobody was altering the footballs during that game.

Tom Brady's legacy is now tarnished, and the NFL may have been able to stop it. Maddie Meyer/Getty Images

To make matters worse, the NFL and one of the game's referees were made aware of the allegations, and yet the footballs still went missing before the game.

Knowing that the Patriots were being accused of deflating footballs and knowing that the footballs went missing, the officials could have easily retested the footballs once they were found. That would have eliminated the weather defense — a central point to the Patriots' defense as evidenced by Robert Kraft's statement following the release of the Wells report — as it is assumed that the only chance to deflate the balls occurred before the game, meaning there would have be very little time between the initial measurements and the retests.

But more important, it would have kept the Patriots from using illegal footballs during one of the most important games of the season.

The report also makes it clear that the NFL should have taken the allegations made by the Colts seriously, noting that the actions of one of the employees accused of altering the footballs, locker room attendant Jim McNally, had come under review of the NFL after allegations arose that he was supplying "non-approved practice balls" in place of approved footballs during a game in 2004.

The report insists that there was "was no 'sting' operation" put in place by the NFL. But if the goal was to catch the Patriots red-handed, it apparently worked.

At the same time, the NFL has another ugly mess that it seems could easily have been avoided.