So much for Roger Goodell’s long-suspected favoritism toward Robert Kraft and the New England Patriots.

That was put to rest late Monday afternoon when the NFL announced it was suspending Patriots quarterback Tom Brady for the first four games of the 2015 season, taking No. 1 and No. 4 draft choices from the team and fining the franchise $1 million because of Deflategate.

Good for Goodell.

This was one of the commissioner’s better days.

It’s not that Goodell had much choice. He had to come down hard on the Patriots. Too many people, inside the NFL and out, were watching. There long has been a belief around the league, including at Pittsburgh Steelers headquarters, that Goodell was too cozy with Kraft, the Patriots owner. One NFL insider described Kraft as “an assistant commissioner” in a GQ article in January about Goodell. There was an overwhelming feeling that one man looked after the other.

A couple of incidents seemed to prove it.

In 2007, Goodell adjudicated the Spygate case by fining Patriots coach Bill Belichick $500,000, stripping the team of a No. 1 pick and fining the franchise $250,000 after Belichick was caught videotaping opposing defensive coaches’ signals. It was bad enough that the punishment was considered light for an organization that won the Super Bowl after the 2001, 2003 and 2004 seasons. Goodell made it much worse by destroying the evidence.

“There should be an asterisk,” former Steelers linebacker Joey Porter said of the Patriots’ championships. “They cheated and they got caught.”

In September, Kraft rushed to the beleaguered Goodell’s defense and described his handling of the Ray Rice domestic-violence case as “excellent.” Rice, then with the Baltimore Ravens, knocked out his then-fianceé inside an Atlantic City, N.J., elevator in February. Goodell suspended him for two games initially, then he made it an indefinite suspension after a video of the incident became public. Many thought Goodell should have been fired.

There still was more Goodell-Kraft relationship talk in January, soon after the NFL announced it was investigating possible football-doctoring by the Patriots during their 45-7 win against the Indianapolis Colts in the AFC Championship Game. On the eve of that game, Goodell attended a party at Kraft’s home and was photographed arm-in-arm with Kraft. That prompted outrage from Seattle Seahawks cornerback Richard Sherman, whose team was to play the Patriots in Super Bowl XLIX. “Talk about a conflict of interest,” he said what many were thinking.

Goodell acknowledged his fondness for Kraft on a personal level but promised to oversee a thorough investigation of Deflategate. “Since he knows me so well, and he knows I am not going to do anything to compromise the integrity of the league, I think he has no doubt that I will do the right thing for the NFL,” Goodell said in his annual address at the Super Bowl.

That seemed like just so much rhetoric until Monday afternoon when the NFL announced its punishment. It came after the release last week of independent investigator Ted Wells’ report that concluded it was “more probable than not” that two Patriots equipment staffers doctored the footballs in the Colts game and that Brady “was at least generally aware” of the rule violation. Who knows? It could have been going on for years.

Kraft looks like a fool. At the Super Bowl, he demanded an apology from the NFL for making the Patriots endure such a frivolous investigation. Brady looks like a liar. He vehemently denied any wrongdoing with the footballs.

But what happened to those balls isn’t what’s important. Many football people will tell you that deflating the balls is no big deal. It’s fair to think Brady wasn’t the first quarterback to prefer balls with less air pressure because they are easier to grip and throw. It’s even more reasonable to think the Patriots weren’t the first team to doctor footballs.

But Brady assured he would get a long suspension by refusing to cooperate with Wells. Who knows what he was trying to hide when he wouldn’t turn over his cell phone records? Maybe it had nothing to do with Deflategate. We are left to speculate, right? We might never know what secrets were in that cell phone.

What we do know is Brady is out for four games, pending appeal, of course. This should have a significant negative impact on the Patriots. The suspension could put their season in jeopardy. The only time they missed the playoffs in the past 12 seasons was in 2008 after Brady blew out a knee in the first game.

Brady’s reputation also is damaged beyond recognition. He is out of his mind if he believes, as he said last week, that the latest Super Bowl win isn’t tainted.

Brady and Belichick always will be in the same dubious Hall of Shame. Belichick, despite four Super Bowl wins, never will be regarded as one of the NFL’s all-time great coaches because of Spygate. “Beli-cheat,” the league’s winningest coach, Don Shula, called him late last year. Now, it’s Brady’s turn. Despite his four Super Bowl wins, he never will be considered as one of the all-time great quarterbacks because of Deflategate. Not even the Goodell-Kraft relationship could save his legacy.

Maybe it really is true what they say:

Cheaters never win in the end.