By Jill Martin

CNN

HOUSTON (CNN) -- New England Patriots owner Robert Kraft got ready to speak. He was on the field, holding the Lamar Hunt Trophy, after his team dominated the Pittsburgh Steelers to win the AFC Championship Game at Gillette Stadium in Foxborough, Massachusetts.

What he then said was viewed as a shot at NFL Commissioner Roger Goodell.

"For a number of reasons, all of you in the stadium understand how big this win was," Kraft said, which drew a roar from the crowd. "But we have to go to Houston and win one (more)."

The Patriots are back in the Super Bowl, and that means Goodell can't hide from them anymore. Or at least that's what it feels like.

"Deflategate" was born a little more than two years ago, the last time Goodell attended a Patriots home game. But soon enough, Goodell, Kraft and Tom Brady will be in the same location: NRG Stadium in Houston at Super Bowl LI.

"I've gotta ask you, you've just gotta be as honest as you can," FOX's Colin Cowherd asked Goodell on Wednesday. "If you handed the trophy to Brady, wouldn't there be a little discomfort, maybe, because of all the talk and the narrative and the media? Would you be slightly uncomfortable for even a moment?"

Goodell didn't hesitate in his answer.

"Not for a second," he said. "This is one of the great opportunities. ... I'm going to be thrilled.

"Tom Brady is one of the all-time greats. He has been for several years. He's on the precipice of at least potentially winning his fifth Super Bowl ring. He's an extraordinary player, great performer and a surefire Hall of Famer, so it would be an honor."

On Friday, Brady said his teammates are all the motivation that he needs for this game.

"I don't get caught up in negativity and bashing other people," he said.

Triumphant return for Brady

It all began Jan. 18, 2015, when the Patriots were accused of using underinflated footballs to gain a competitive advantage in their 45-7 win against the Indianapolis Colts in the AFC Championship Game. The NFL said there would be an investigation led by Ted Wells, and New England went on to win Super Bowl XLIX, in which Brady was named MVP. The Patriots quarterback denied wrongdoing.

Following the Wells report, the NFL imposed a four-game suspension on Brady and fined the Patriots $1 million. The team also had to forfeit its first-round selection in the 2016 NFL Draft and its fourth-round selection in the 2017 NFL Draft. Brady appealed his suspension, but Goodell upheld it.

Then there was that whole legal thing between the two of them. The dispute went to federal court, where the suspension was nullified. The NFL appealed the decision. The league won, and the punishment was reinstated. On July 15, Brady said in a Facebook post he would not pursue further legal action.

Brady served his four-game ban and returned to throw 28 touchdowns and just two interceptions in the regular season. The Patriots went 14-2 and secured the top seed in the AFC.

After winning the AFC Championship Game, Brady was asked how satisfying it was for him personally to get back to the Super Bowl having been suspended this season. Brady deflected, saying it took a lot of people and hard work over the course of many months.

"There are only two teams left standing, and I'm happy we're one of them," Brady said. "That's what our goal is, and it's nice to be able to achieve that."

A day later, on the quarterback's weekly appearance on WEEI's Kirk and Callahan show, Brady was asked what he would say to Goodell if the commissioner handed him the trophy.

"Hopefully we can finish the deal," Brady said. "Hopefully we can finish it off and we'll see. Maybe I'll tell you after. But I don't want to get into winning something before we've won it, because it's going to be hard to win this thing."

Was Goodell ducking Foxborough?

Typically, Goodell attends big games on the schedule, such as the season opener for the defending Super Bowl champions. But in 2015, he didn't go to Gillette for the Patriots' banner ceremony in Week 1.

During the playoffs, Goodell traveled to a game each week. In this season's divisional round, he went to Atlanta for the Falcons' game against the Seattle Seahawks. The following week for the NFC and AFC championship games, Goodell had two choices. Once again, he opted for Atlanta instead of going to Foxborough.

At Gillette Stadium that night, fans chanted, "Roger!" and "Where is Roger?"

Brady said after the game he didn't hear the chanting.

CNN reached out to the NFL on Wednesday to get a comment from Goodell about not going to Foxborough, but on that same day, he talked about it with Cowherd.

"We had two great games," Goodell said to Cowherd. "I was in Boston two years ago for the divisional and the championship games. I try to get to as many stadiums as I can, but, you know, we have got two great games and you've got to choose. And frankly, the focus should be on the players, the coaches and the great game. And that's the way it was this week, and that's the way it should be."

And what about Kraft? Does Goodell think it's true he is displeased with him?

"I wouldn't be doing my job if somebody wasn't unhappy with a decision that you make or what you're doing it," Goodell said in the Cowherd interview. "Robert and I can disagree about things. We have a healthy respect for one another, but that's true with any owner. That doesn't affect my relationship or the fact that we work together to try to make the NFL better ultimately."