Stanton says Marlins officials threatened to keep him for the rest of his career.
Jeter said the deal with his former team was the best one available to the Marlins, giving them much-needed financial flexibility and upgrading a weak farm system. The Marlins' new CEO made his comments shortly before Stanton held a news conference at baseball's winter meetings in Lake Buena Vista to discuss a trade being celebrated in New York but panned by beleaguered Marlins fans.
Jeter wants to reduce his revenue-starved franchise's payroll by at least 20 percent to $90 million or less, and Stanton will make $25 million next year. But trading him wasn't a given, Jeter said.
"I told him, 'When we acquired this team, our thoughts were that you were going to be with us,'" Jeter said. "I relayed to him we wanted him to be a part of the organization, but it's his choice. He said he wanted to move on. There were three great options for him, and he chose which one he wanted to go to."
Stanton had a no-trade clause in his record $325 million, 13-year contract, for which he is owed $295 million over the next 10 seasons. Last week he turned down prospective trades to St. Louis and San Francisco before accepting the Yankees' deal.
At Stanton's news conference, the All-Star right fielder confirmed he opted to move on from Miami in a meeting with Jeter.
"We spoke about the direction of the team," Stanton said. "I wanted us to go forward. I thought our lineup was legit, and we needed help with our pitchers, and we needed to add rather than subtract. The way they wanted to go was to subtract. So I let that be known that I didn't want to be part of another rebuild, another losing season, and that's almost a guaranteed losing season."
Stanton never played on a winning team in eight years with the Marlins, and he said they threatened to keep him for the rest of his career if he didn't accept a trade to the Cardinals or Giants. But he wasn't swayed.
"It doesn't matter what the dynamic was," he said with a stern expression. "You're not going to force me to do anything."
Stanton said he considered the threat unfair.
"Yeah, after being a part of the organization for so long, and everything I've done there," he said.
In an Instagram post, Stanton thanked Marlins fans and the organization, but he also referred to the "roller coaster years" under previous owner Jeffrey Loria.
"I've always tried to be as professional as possible during the unprofessional, circus times there!" he wrote.
Jeter has drawn criticism for the trade and other moves early in his tenure as an owner, but he said he would have done nothing different regarding Stanton. The Marlins acquired two prospects and second baseman Starlin Castro.
"Contrary to popular belief, we were not stuck with this deal," Jeter said. "This was the best deal out of the three for our organization. ... We think we got some good prospects in return."
Further payroll paring is likely at the winter meetings, which Jeter is not attending. Castro and outfielders Marcell Ozuna and Christian Yelich are believed to be on the trading block.
But the departure of Stanton increases the Marlins' options.
"It's tough to have one player be such a huge part of your payroll," Jeter said.
The payroll purge is the latest in a series for the Marlins, who haven't been to the playoffs since 2003 and have finished last in the NL in attendance 12 of the past 13 years.
With Stanton gone, neither the team's record nor support by antagonized fans is likely to improve soon.
"Look, I get it. They're upset. They're passionate," Jeter said. "That's what makes them fans. But the bottom line is the fans want to see a winning product on the field. They haven't seen a winning product on the field.
"To do this, we're going to have to make some moves and build this organization. I would tell the fans: Be patient. What had been in place has not been working, and we need to fix that."
Said Stanton: "I would advise them not to give up. Just keep hope. Maybe watch from afar, if you're going to watch."
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