Mets designated hitter Yoenis Cespedes returns to the dugout after...

Mets designated hitter Yoenis Cespedes returns to the dugout after he strikes out looking against the Boston Red Sox during the second inning of an MLB baseball game at Citi Field on Thursday, July 30, 2020. Credit: Kathleen Malone-Van Dyke

Yoenis Cespedes’ turbulent tenure with the Mets all but ended Sunday when he left the team without warning — and hours later communicated that he was opting out of the rest of the 2020 season.

A bizarre three hours began after the top of the first inning, when the Mets released a statement saying Cespedes did not show up to the ballpark and they were unable to contact him. It ended after a 4-0 loss to the Braves, when general manager Brodie Van Wagenen revealed that Cespedes’ representatives told the Mets he was done for the year due to concerns regarding the coronavirus pandemic.

Cespedes also was facing the possibility of diminished playing time as he struggled at the plate, playing regularly for the first time in more than two years. His contract included lots of bonuses attached mostly to at-bat totals.

Van Wagenen said he had no idea Cespedes was about to abandon the team. He found out about the official opt out toward the end of the game.

“We support everybody’s and every player’s right to make this type of decision,” Van Wagenen said. “It was surprising, without question.”

Roc Nation, Cespedes’ agency, did not respond to requests for comment.

Technically, Cespedes will be placed on the restricted list and remain under contract through the end of the season. He will not earn the rest of his salary.

This effectively marks the end of the four-year, $110 million deal — a contract negotiated on his behalf by Van Wagenen, his agent at the time — Cespedes signed after the 2016 season. He played 127 games in those four seasons. In between, there were pseudo-controversies over his conditioning and golf habit, a series of stints on the injured list, a surgery on each heel, an encounter with a wild boar on his Florida ranch, a resulting broken ankle that required another surgery and a renegotiated contract.

Cespedes originally was due to earn $29.5 million this year. That was reduced to $6 million — plus lots of potential bonuses — due to the boar incident. After the season’s pandemic delay led to all salary being prorated, he had a base pay of $2.22 million. Now, he gets about $611,000 for nine games.

“It’s disappointing,” Van Wagenen said of the whole saga. “Yo’s a great player that everyone enjoyed watching play when he was at his best. There was optimism for his return. I know how hard he worked in his rehab to get back to this point, and I know this is a disappointing end to at least his four-year agreement with the Mets.”

Van Wagenen said he was not angry with how Cespedes handled opting out. But he was confused and concerned for part of Sunday.

When the enigmatic outfielder did not show up to Truist Park in Atlanta Sunday morning, the Mets released a statement indicating they did not know where he was. At the time, according to Van Wagenen, they were unsure of his well-being.

“As of game time, Yoenis Cespedes has not reported to the ballpark today,” the statement, attributed to Van Wagenen, read. “He did not reach out to management with any explanation for his absence. Our attempts to contact him have been unsuccessful.”

The Mets sent security to his room at the team hotel. Neither he nor his belongings were there, Van Wagenen said.

About an hour after the original statement, a Mets source said, “At this time, we have no reason to believe Yoenis’ safety is at risk.”

Van Wagenen said the initial announcement about Cespedes being AWOL — apparently released without knowing if he was in danger — was made in a desire to be “transparent” and “provide information in real time.”

“There was no hidden agenda,” Van Wagenen said. “There was no attempt to mislead by any stretch of the imagination. Just providing information as we had it.”

Cespedes ended his two-year absence from the majors on Opening Day, when he homered to account for the only run in the Mets’ win. But in starting eight of the first nine games, he hit only .161 with a .235 OBP and .387 slugging percentage. He struck out 15 times in 31 at-bats.

With J.D. Davis, Dominic Smith and others competing for playing time, Cespedes’ everyday spot in the lineup wasn’t guaranteed.

“I had conversations with him over the last couple of days to reassure him that our job was to try to put the best team on the field every day,” Van Wagenen said. “Luis had the power and the authority to try to do that with the lineup and … he was certainly given every opportunity to try and help us perform.”

Manager Luis Rojas said before the game: “He’s not starting in the nine, but we want to get him in there and get the at-bats that he needs in order to get hot.”

Rojas said his last conversations with Cespedes came Saturday. They talked about how he felt at the plate, his upcoming work in the outfield and that day’s opposing pitcher — but did not talk about or even hint at lessened playing time, according to Rojas.

A day later, Cespedes was done, apparently scared by the pandemic.

Rojas said Cespedes’ actions did not upset him.

“This is part of what’s going on right now in the world,” Rojas said. “This is part of what’s going on right now in this league.”

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