SAN FRANCISCO – Now that Patriots owner Robert Kraft is not appealing his team’s punishments in the deflated footballs scandal, only his quarterback’s challenge remains.

Moments after Kraft said Tuesday he won’t oppose the $1 million fine and loss of two draft choices the NFL penalized the team for its role in using underinflated footballs in the AFC championship game, the players’ union reasserted that Tom Brady’s appeal will go forward.

New England Patriots owner Robert Kraft speaks at the NFL owners meetings in San Francisco on Tuesday, when he announced that he is not appealing his team's punishments in the deflated footballs scandal.

Brady, the MVP of February’s Super Bowl and one of the league’s biggest stars, has been suspended for the first four games of the 2015 season by the NFL.

So while Kraft sought to end the “dialogue and rhetoric,” it’s certain “Deflategate” won’t disappear anytime soon.

At the owners meetings, Kraft said he was putting the league before his franchise because “at no time should the agenda of one team outweigh the collective good of the 32.”

The Patriots will lose a first-round draft pick next year and a fourth-rounder in 2017.

“When the discipline camea out, I felt it was way over the top,” Kraft said, adding that if he had made his decision last week, “I think maybe it might have been a different one.”

But after further consideration, he cited “believing in the strength of the (NFL) partnership and the 32 teams” for dropping any appeal plans.

Kraft also recognized the powers given to Commissioner Roger Goodell.

“Although I might disagree in what is decided, I do have respect for the commissioner, and believe he is doing what he perceives to be in the best interest of the 32,” Kraft added.

Kraft would not take any questions Tuesday about his decision nor about Brady’s appeal, which will be heard by Goodell. But he has said he’s convinced Brady played no part in deflating the footballs.

Brady’s appeal will be heard within the next week. On Tuesday, the union formally requested that Goodell recuse himself from serving as arbitrator, saying he is not impartial and that he is a “central witness in the appeal.”

An NFL spokesman said the league would have no comment.

Kraft was livid when the Wells Report, which was commissioned by the NFL and took nearly four months to compile, contained what he termed “all circumstantial, no hard evidence.” He said Tuesday that “the entire process has taken too long; it’s four months after the AFC championship game, and we are still talking about air pressure … in footballs.”

This is the second time in Kraft’s 21 years as owner that the Patriots have been disciplined for breaking NFL rules. In 2007, they were penalized for videotaping New York Jets signals during a game. They didn’t challenge fines of $500,000 against coach Bill Belichick and $250,000 against the club, along with the loss of a first-round draft pick.

Kraft has long been a confidant and adviser to Goodell and was one of the owners who championed Goodell to replace Paul Tagliabue in 2006. Kraft also was one of the leaders in getting key owners and the union together to end the 2011 lockout, and he’s been a major force in negotiations with TV networks.

In other words, a team player, something he stressed in his short news conference Tuesday.

“What I’ve learned over the last 21 years is the heart and soul and strength of the NFL,” he said, “is the partnership of 32 teams.”

Outside the Ritz-Carlton, Chase Bender, a 21-year-old senior at Cal-Berkeley who identified himself as a football fan, made his own statement. He had a pile of deflated footballs and a bag full of more, along with a Patriots helmet.

Bender began sitting outside the hotel around 10 a.m. with hopes of having a word with Kraft, or at least get him to sign the helmet.

“I don’t really think they cheated,” he said. “If they did, just say sorry and that you know it was wrong, accept your penalty and get on with it.”

AP Sports Writer Janie McCauley contributed to this story.