In the end, it all came down to Jeff.

Multiple sources have confirmed to The Post that the biggest unsolvable issue in the now-all-but-dead sale of the New York Mets to billionaire hedge fund manager Steve Cohen was the role that team heir and COO Jeff Wilpon would have in the transition of power and beyond.

At the late stages of his agreement to buy 80 percent of the franchise for $2.6 billion, Cohen was informed by Fred and Jeff Wilpon that their plan was for Jeff to maintain total operational control of the Mets throughout the pre-agreed-to five-year transition period and then maintain a senior role within the organization even after Cohen took over.

While it is unclear whether the Wilpons, who said Thursday night they still plan to sell the team, sought to keep the COO title for Jeff after the transition, sources uniformly agree Jeff wanted to be part of the decision-making under Cohen’s ownership.

Asked at the Major League Baseball owners’ meetings Thursday in Orlando, Fla., if he expected the sale to come together somehow, commissioner Rob Manfred said, “All I can tell you is right now, my belief is there is not going to be a transaction — and my soothsaying is not great.

“I don’t know what’s going to happen,” Manfred added, to laughter. “As of right now, it’s my belief that the transaction is not going forward.”

Manfred also said that “based on conversations with the buyer and the seller on an ongoing basis [that] the assertion that the transaction fell apart because of something the Wilpons did is completely and utterly unfair.”

One source familiar with the talks said Cohen was trying to change the financial terms of the deal.

However, one former Mets employee told The Post that it was almost inconceivable to think that a deal would have been struck without a role for Jeff.

“This guy has never done anything in his life other than play a week of minor league baseball and work for his dad,” said the former Mets staffer. “The Mets are his life. He can’t do anything else.”

By all accounts, Jeff’s current leadership of the organization is extremely hands-on. Every facet of the team, from baseball operations to marketing, is known to be under his purview.

“He is the owner and the de facto general manager,” said one source close to the team. “He does not want to give that up, even if everyone around him does.”

Cohen himself confirmed in a statement Thursday night that the deal is in fact dead.

“I’m very disappointed we couldn’t work out a deal,” Cohen wrote before taking a thinly veiled shot at the Wilpons. “But as an 8% holder I’m looking forward to a higher bid for the team.”

The billionaire financier also thanked Mets fans who have been begging him to move forward with the purchase on sports radio and social media, many of whom have also been savaging the Wilpons and Major League Baseball for the deal failing to materialize.

“I want to thank the fans for their support and the respect they showed me and I want to thank Commissioner Manfred and MLB for their support through the process,” stated Cohen. “I gave it my best shot.”

The Mets released a statement on behalf of Sterling Partners, the Wilpons’ entity which owns the Mets, shortly after Cohen on Thursday.

“The transaction between Sterling and Steve Cohen was a highly complicated one. Despite the efforts of the parties over the past several months, it became apparent that the transaction as contemplated would have been too difficult to execute. Sterling intends now to pursue a new transaction and has engaged Allen & Company to manage that process.”

Sources familiar with Wilpons’ thinking tell The Post that they are upset and angry with the death of this deal coming out in the press and that they are as ready to kill this deal as Cohen is. With the fan base getting increasingly angry on local sports radio and social media, begging the Wilpons to sell the team to a hedge-funder Mets fan worth $13 billion, Fred and Jeff are livid at the situation and want it to end.

Making matters more frustrating, both sides remain muzzled by what appears to be an ironclad non-disclosure agreement.

But one of those sources also mused how this extremely public pre-divorce is playing out at the owners’ meetings.

“You just wonder if the other owners tell them to just get this done,” the source said. “It’s so much money.”

Fred Wilpon declined comment to The Post at the meetings. Jeff Wilpon did not respond to a request for comment from The Post.

— Additional reporting by Ken Davidoff in Orlando, Fla.