Pete Alonso’s free-agent saga is over, and he ended up right where he started.

The first baseman agreed to a two-year, $54 million contract with the Mets, The Post’s Jon Heyman reported.

The deal, agreed to Wednesday night, was pending a physical and includes an opt-out after this season, so Alonso can hit the open market again if he puts up better numbers than he did in a subpar 2024.

He’ll make $30 million this season, with a $24 million player option for 2026, as the Mets waited out Alonso, who couldn’t find a more lucrative deal elsewhere.

Alonso was also offered a three-year deal with the Mets worth $71 million, but opted for a two-year contract with a higher AAV and the opt-out.

It ends what was a drawn-out process for the 30-year-old who has spent his entire career with the Mets after being drafted in the second round in 2016.

Alonso turned down a seven-year, $158 million extension in 2023 before hiring agent Scott Boras.

But Alonso then had the worst season of his career last year, with 34 homers and a .788 OPS.

That, coupled with the fact he turned 30 this offseason and president of baseball operations David Stearns has shown he doesn’t like to sign players in that age range to long-term deals, made for a questionable reunion.

“Personally, this has been an exhausting conversation and negotiation,’’ Mets owner Steve Cohen said at Citi Field on Jan. 25. “[Juan] Soto was tough, this is worse.”

As The Post reported, the Mets previously offered Alonso a three-year deal worth around $68 million to $70 million this offseason, which Alonso’s camp rejected.

When that was turned down in mid-January, the Mets made moves in anticipation of Alonso heading elsewhere by re-signing Jesse Winker and bringing in another free agent, A.J. Minter, to bolster their bullpen.

They also told Mark Vientos and Brett Baty to take grounders at first base this offseason, though that would have left the Mets with an infield with inexperienced players on both corners of the diamond.

And even last week, Cohen added, “I will never say ‘no’ — there’s always a possibility — but the reality is, we’re moving forward. As we continue to bring in players, the reality is it becomes harder to fit Pete into what is a very expensive group of players that we already have.”

But they eventually got back together as other clubs were perhaps scared off because Alonso received a qualifying offer from the Mets, which would have required draft-pick compensation from the team that signed him.

So now the team that reached the NLCS before falling to the Dodgers will bring back a similar roster — plus the addition of Soto.

Though the free-spending Dodgers no doubt remain the favorites in the National League, the Mets now aren’t far behind.

For Alonso, it’s a tough end to his first foray into free agency and he’ll have to hope for a bounce-back season that could put him back into free agency next offseason in a better position — similar to what other Boras clients, Matt Chapman and Blake Snell, did with the Giants late last offseason.

Both then signed lucrative long-term deals — Chapman an extension with San Francisco and Snell with the Dodgers.

Alonso will have Soto in the lineup with him, which figures to help his production, as it did for Aaron Judge in The Bronx last season.

For the Mets, it’s a clear victory, as they are certainly better with Alonso’s big bat at first and Vientos at third than the alternative.

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The Mets announced right-hander Dylan Covey and infielder Luis De Los Santos were outrighted to Triple-A Syracuse.